studium 0.10.1

data/lib/studium/exam_topics/biochips

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+# =========================================================================== #
+# === Biochips
+#
+# This will be about Biochips and Microarrays.
+# =========================================================================== #
+
+- In microfluidics, for lab-on-a-chip: name three parameters for the <one>integration of functionality</one>. A: (1) <one>compactness</one> (2) <one>parallelization</one> (3) <one>high-throughput</one>
+- In <one>live cell microarrays</one>, we may wish to put ESCs onto the surface, but prior to that, we may have to coat the surface of our substrate with ...? <one>Fibronectin</one>.
+- Is a <one>reference genome</one> necessary for the design of probes of a DNA microarray? Yes.
+- Why are <one>Carbohydrate Microarrays</one> typically used? This is to study <one>post-translational modifications</one>.
+- Nenne einen Vorteil der Organchips gegenüber Tierversuchen. A: Man kann, dank der Organchips, mit menschlichen Zellen arbeiten.
+- Wann mögen wir den <tomato>MethylScope Microarray</tomato> einsetzen? Wenn wir einen Tumor mit gesundem Gewebe vergleichen möchten.
+- TMAs are ... what microarrays? <tomato>Tissue microarrays</tomato<: 
+- In DNA-microarrays, what do we mean with the "target"? These are the amplified, labeled cDNAs generated from the total RNA from a cell or tissue.
+- The concept and methodology of "protein microarrays" was first introduced and illustrated in ... ? "antibody microarrays".
+- In microarrays, what is meant with the term "direct labeling"? This is when we put e. g. a "fluorophore" on primers or nucleotides directly.
+- Name a microarray that starts with the letter "T". A: "Tilingarrays".
+- Which person invented the microarray technology? "Stephen Fodor".
+- Photolitography is a process based on semiconductor technology. It uses light but also ... ? "Light-blocking masks".
+- Name three different "Microarray manufacturers". A: (1) Affymetrix (2) Agilent (3) Illumina
+- In Biochips design, why may we want to swap dyes? The dyes may behave differently; this way we can assess whether they do.
+- In Biochip design, what do we mean with "MDMs"? These are "microbial diagnostic microarrays".
+- In Biochip technology, we may have to check "data quality" on different levels. Name three different levels here. A: (1) Probe level (2) Array level (3) Gene level
+- In Biochip design, we may use spaces, after a NH2 group at one end. This may be Thymidine. How many Thymidines are used? About 12 T.
+- How are microarrays read out? Microarrays are read out via a "laser-based fluorescence scanner".
+- What is the "central assumption" of Gene Expression Microarrays? That the level of a given mRNA is positively correlated with the expression of the associated protein.
+- What does an "expression array" measure? It measures the amount and type of mRNA transcripts.
+- If we may wish to do "patient stratification", which microarray method may we employ? An "antibody microarray".
+- In Biochips, contactless printing requires humidity of ... n%? About 65%.
+- In Biochips, which two different pins are oten used for "contact printing"? (1) split pin (2) solid pin
+- In "contact printing" for biochips, what is the droplet volume (from-to)? About 400-600 pl.
+- In Biochip design, the 16S rRNA is often used for phylogeny, but it is not always ideal. Name an intrinsic problem that the 16S rRNA has. A: It can not provide for "strain-specific information".
+- A phylogenetic marker should ... ? Reflect taxonomy.
+- Name 3 disadvantages of "spotted cDNA microarrays". A: (1) Sequence verification (2) poor surface-adhesion properties (3) The data can be variable
+- For microarrays, we may need a "molecular marker". What do we mean with this? This is a DNA sequence, which is specific for a certain phenotype or genotype.
+- In Biochips, how do we call the method that can find a spot, in general? This is called "spot identification".
+- What must come before applying a microarray to real datasets? Validation.
+- How many cDNA probes can be easily put on an average microarray? About 20.000 cDNAs.
+- Give a reason why "diagnostic microarrays" are used. A: So that we can detect disease-related genes.
+- Give on example for an "alternative microarray format". A: Clondiag, the "ArrayTube".
+- In Macroarrays, probes are on ...? The membrane.
+- Name two fixatives commonly used for CMAs ("cell microarrays"). A: (1) formalin (2) paraformaldehyde
+- In Biochip design, when we use "mixed-genome microarrays", name an advantage in their construction. A: We do not need to have any "a priori" knowledge about the genomes, in order to construct these microarrays.
+- In Biochip sciences, what does "MGM" stand for? Mixed-genome microarrays. URL: https://www.ncbi.nlm.nih.gov/pubmed/12574259  
+- In Biochip design, we may use the material "PMMA". What does this abbreviation stand for? Polymethymethacrylate.
+- Name three different types of microarrays. A: (1) DNA Microarrays (2) Peptide Microarrays (3) Carbohydrate Microarrays
+- Why do Biochips usually use plastic rather than glass? Because plastic is much cheaper than glass.
+- The two major dyes used in Biochips, Cy3 and Cy5, have which colour, respectively? (1) Cy3: green dye (2) Cy5: red   dye
+- In Biochip-design, the oligonucleotides (mers) should not be too short. Why not? Because too short mers tend to be too unspecific.
+- Cartridge-based microarrays are typically surrounded via ...? A plastic housing.
+- Name 3 different "non-contact printing" ways to create microarrays. A: (1) Thermal (2) Piezo (3) Valve
+- Who developed the "PhyloChip"? Affymetrix.
+- The PhyloChip from Affymetrix uses n-mers biochips? 25-mers.
+- In probe design of biochips, why are different lengths used for different oligos? So that they have, roughly, the same melting temperatures
+- SSELO is a novel labeling approach in biochips design. What does SSELO stand for? "Sequence-specific end-labeling of oligonucleotides".
+- Name the four major "Unique Selling Points" of Biochips. A: (1) parallel approach (2) miniaturization (3) automation (4) integration of functions
+- In Biochips, what are "PM probes"? Perfectlymatching probes. URL: https://www.vsni.co.uk/software/genstat/htmlhelp/marray/AffymetrixChips.htm
+- In Biochips, what are "CMAs"? These are "cell microarrays".
+- Can we use the DNA microarray to determine whether the DNA from a particular individual contains a mutation in different genes? Yes. In fact, this can be used to look at differenial expressions between BRCA1 and BRCA2.
+- What is "fold change" in context of a DNA microarray experiment? Fold change is a measure describing how much a quantity changes going from an initial to a final value. For instance, an initial value of 30 and a final value of 60 corresponds to a fold change of 1, or in common terms, a "one-fold increase".
+- "Experimental design" of microarray experiments has which 3 different design possibilities? (1) Direct Design (2) Reference Design (3) Loop Design
+- For "one colour arrays", of DNA microarrays, what do we actually compare? We compare different arrays here.
+- In a microarray experiment, we may use the dye C3 and C5. Which colour do they display usually? (a) Cy3: Green (b) Cy5: Red
+- What means "limma"? Linear models for microarray data.
+- Welche andere Technik kombiniert die ChIP-chip? Microarray Technologie.
+- A. W. für "Microarrays" in der Gentechnik? "lab-on-a-chip"
+- In Chip-Design, was heisst "LOC"? Lab-on-a-Chip.
+- Was ist am teuersten bei einem Microarray-Experiment? Die Farbstoffe.
+- We may use expression profiles, such as via a "DNA microarray". When we use a one-colour array, what exactly do we measure there? Only the signal intensities will be measured.
+- Why is glass used rather than silica in microarray-chip design? Because we can see through glass; we can't see through silica.
+- In Chip-Design, what means "OOAC"? Organ-on-a-Chip.
+- In Chip-Design, what means "TMAs"? Tissue microrrays.
+- In what year was the first genechip, a prototype, developed? In 1989.
+- When were the first cDNA arrays developed? In 1994, at the Stanford University.
+- Name a "clinically validated HPV genotyping assay". A: The PapilloCheck.
+- In a standard microarray, if we see a yellow dot, what does this mean? This means "no net change", thus uninteresting to us.
+- What means "DArT" in biochips technology? Diversity Arrays Technology. URL: https://en.wikipedia.org/wiki/Diversity_Arrays_Technology
+- DArT is useful for ...? DArT is useful for large gnomes, such as plant genomes.

data/lib/studium/exam_topics/bioelektrochemie

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+# =========================================================================== #
+# === Bioelektrochemie tag.
+#
+# Bioele tag. Muskel tag- und das dann auslagern.
+# =========================================================================== #
+
+- Wo (anatomisch betrachtet) finden wir die <one>Purkinje-Fäden</one>? Im <one>Herzen</one>.
+- Does <orange>pure water</orange> conduct electricity? No.
+- Was muss Elektrokommunikation bei den Tieren leisten? Die Signalübertragung muss über lange Strecken schnell und ohne Verlust von Information erfolgen.
+- Was ist die "Depolarisation"? Das ist die Veränderung eines Membranpotentials, ausgehend vom Ruhepotential bei ca. -80 mV, hin zu positiveren Werten.
+- The human cortex is organized into how many layers? Into 6 layers.
+- Welche 3 wichtigen Bereiche im Neuron muss ein Aktionspotential durchlaufen um weitergeschickt zu werden? (1) Soma (2) Axonhügel (3) Axon
+- Wozu führt die Depolarisation der Nervenzelle? Zur Auslösung des Aktionspotentials.
+- Poren in Neuronen haben einen kugelförmigen Anhang. Wieso? Dieser Anhang verschliesst die Pore des Kanalproteins nach 1-3 ms, und stoppt so den Na-Einstrom.
+- Gib ein Beispiel für Werkzeuggebrauch bei Säugetieren die oft im Wasser leben. A: Seeotter, der einen Stein verwendet um Muscheln zu knacken.
+- Wieso werden wir die PET-Tomografie in der Neurobiologie an? Weil wir damit Bereiche hoher Stoffwechselaktivität aufspüren können.
+- Wie nenn man die Distanz zwischen 2 Z-Scheiben? Sarkomer.
+- Wieso ist das Gift der Kegelschnecke so wirksam? Es unterbricht sowohl die elektrische als auch die chemische Signalgebung der Neurone.
+- A. W. für "erregende" Synapse? Exzitatorische Synapse.
+- Was ist der "Electroplax"? Das elektrische Organ des Zitteraals.
+- Wie nimmt eine Nervenzelle Information wahr? Über ihre Dendriten.
+- Was ist "Sphyrna lewini"? Der Hammerhai.
+- W. h. "Impedanz"? Widerstand.
+- Was sind die "Ryanodinrezeptoren"? Das sind Zellen im Herzmuskelzellen, die calciumgesteuerte Calciumkanäle sind.
+- Welche 3 Kontraktionsmöglichkeiten hat ein Skelettmuskel? (1) isoton (2) isometrisch (3) auxoton
+- Was ist die Aufgabe der "Muskelspindeln"? Sie messen den Dehnungszustand von Skelettmuskeln.
+- Golgi Staining wurde wann erfunden? 1873.
+- Die elektromechanische Kopplung verläuft im Herzmuskel ganz ähnlich wie im Skelettmuskel. Es gibt aber einen wichtigen Unterschied - welchen? Ein Unterschied besteht bei der Calciumfreisetzung. 
+- Vergleiche das verwendete Aktionpotential in Herzen (beim Sinusknoten) mit dem Aktionspotential in Nervenzellen. A: Das Aktionspotential in Nervenzellen ist 100-1000 mal schneller.
+- Haben die Zellen des Sinusknoten die Möglichkeit, die Erregung einzustellen? Nein, sie haben keinen Ruhezustand. Das wäre ja auch kontraproduktiv wenn das Herz aufhört zu schlagen.
+- Was macht der Sinusknoten? Der gibt den Herzmuskelzellen den Takt vor.
+- Was sind "Schrittmacherzellen"? Das sind Zellen des Herzmuskelgewebes.
+- Beruht die rhythmische Erregung des Herzens auf neuronaler Aktivität? Nein, sie beruht ausschliesslich auf muskulärer Aktivität = myogene Authorhythmie.
+- Was machen Oligodendrocytes? Produzieren Myelin.
+- Welcher Neurotransmitter-Rezeptor war der erste der gereinigt wurde? Der Nicotinic Acetylcholine Receptor.
+- Die Synthese von GABA benötigt welche Aminosäure? Glutamate.
+- Welches Element wird oft in der PET-Tomografie eingesetzt? 18 F.
+- Besitzen die im Wasser lebenden, mehrzelligen Schwämme ein Nervensystem? Nein.
+- A. W. für "ruhende Nervenzellen"? Terminal differenziert.
+- Neurone unterscheiden sich hinsichtlich ihres Aufbaus, dabei kann man sie optisch aufgrund der Anzahl Fortsätze klassifizieren. Nennen Sie die 4 Gruppen hierzu. A: (1) Unipolar (2) Bipolar (3) Pseudounipolare (4) Multipolare
+- Nenne 3 wichtige Parameter der Grundstoffwechselrate! A: Temperatur, Körpermasse, Gehirngrösse.
+- Aplysia hat n Nervenzellen? 20.000 Nervenzellen.
+- Im Aktionspotenzial wird die Membran für Na+ Ionen durchlässig. Für wie lange? Für ein bis zwei Millisekunden wird die Membran durchlässig.
+- Aktionspotentiale erfolgen durch die Öffnung von Natriumkanälen, dadurch strömen positiv geladene Natrium-Ionen in die Zelle. Wie ändert sich das Membranpotential (von, bis)? Das Potential ändert sich von -80 mV auf +30 mV, in der sogenannten "Depolarisationphase". Die Kanäle werden im Anschluss danach inaktiviert.
+- Wieso kann das Herz gleichmäßig schlagen? Die Muskelfasern der Wände der beiden Herzkammern sind miteinander verbunden. Aus diesem Grund erfasst eine Erregung immer das gesamte Herz; das Herz verhält sich wie ein "funktionelles Synzytium". 
+- A. W. für "Ionenpaarbildung"? Assoziate.
+- Welche 2 Signaltypen existieren bei der Kommunikation über Neurone? (1) elektrische Signale: werden über weite Strecken fortgeleitet (2) chemische Signale: werden auf Kurzstrecken eingesetzt
+- Was passiert wenn wir einen Ca2+ Strom in eine Nervenendigung einleiten? Dies führt zur Fusion von Transmitterhaltigen Vesikeln mit der präsynaptischen Membran. Diese Vesikel schütten ihren Inhalt, Acetylcholin, in den synaptischen Spalt aus.
+- Es gibt "elektronenleitende Phasen", Leiter der 1. Art. Gib vier Beispiele hierzu. A: (1) Metalle (2) Halbleiter (3) organische Polymere (4) Ionisierte Gase (Plasma)
+- Was ist die Voraussetzung für die elektrische Stromleitung? Das Vorhandensein von freien geladenen und beweglichen Teilchen.
+- Dielektrizitätskonstante von Wasser? 80.
+- Was sagt die "Hydratationszahl" aus? Die Anzahl der Wassermoleküle in der 1. Sphäre.
+- Wie konnte man die zellulären Vorgänge bei der Muskelkontraktion aufklären? Durch Isolierung des Proteins Aequorin. Bei Kontakt mit Ca2+ emittiert Aequorin bläuliches Licht.
+- Zeigt Aequorin Fluoreszenz? Nein, es zeigt Chemilumineszenz, das heisst die Lichtemission wird nicht durch Absorption von Licht stimuliert (wie bei der Fluoreszenz) sondern durch eine chemische Reaktion 
+- in diesem Fall durch die Bindung von Ca2+-Ionen.
+- Bei den Muskelfasern, wieso heissen die T-Tubuli so? Transversales, tubuläres System.

data/lib/studium/exam_topics/biofilms

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+# =========================================================================== #
+# === Biofilms
+# =========================================================================== #
+
+- "Mature Biofilms" produce what, that could be called "impressive"? "Biofilm towers".
+- In a biofilm, what may flow through its channel? "Nutrients".
+- Does "quorum sensing" occur in biofilm formation? Yes.
+- Give another term for "biofilm development". A: The "biofilm life cycle".
+- In nature, where do biofilms usually form? Where food is abundant, e. g. when there are plentiful nutrients.
+- What do bacteria often do before "biofilm formation" begins? They "secrete (exo)polysaccharides".
+- A biofilm increases resistance of bacteria? Yes; it "increase the reistance to antibiotics", for example.
+- One characteristic feature of "Biofilm Formation"? Marked increase in "Antibiotic Tolerance".
+- Give a very important reason as to why bacteria make use of a "biofilm". A: So that these bacteria can stay where food is abundant and plentiful.
+- Biofilms can "damage non-biological systems", such as ... which fairly big system? "Ventilators". URL: https://www.ncbi.nlm.nih.gov/pubmed/27831764
+- Pseudomonas aeruginosa ist ein berühmt-berüchtigter Biofilm-Former. Was ist das "major signaling molecule" in diesem Bakterium? "Homoserine Lactone".
+- Biofilms contain what? Biofilms contain microbial cells and exopolymeric substances (EPS).
+- Nenne möglichst viele Vorteile von Biofilmen. A: Nährstoffe werden festgesetzt. er vereinfacht intercellular signaling zwischen Bakterien und auch den Austausch von Genen ("close proximy helps genetic exchange".) Der Biofilm schützt gegen das Immunsystem (defence), Biofilme mögen der bevorzugte Weg sein wie Bakterien leben (die Laborkulturen sind hingegen wohl Artefakte), auch hilft er den Bakterien an Ort und Stelle zu verbleiben ("remain at a favourable niche"), z. Bsp in fliessenden Systemen, oder verhaftet als Zahnbelag oder medizinischen Implantaten.
+- Name an important part of bacterial biofilms that does not contain cells. A: The exopolymeric substances.
+- In "Biofilm Formation", name the three general steps. A: (1) Attachment (2) Colonization (3) Development
+- Nenne eine Chemikalie die gegen Biofilm-Formation hilft (Stichwort: "biofilm inhibition"). A: Furanones.
+- Nenne die 3 steps bei Biofilm-Formation. A: Attachment, Colonization, Development.
+- Welche konkrete Krankheit mag durch Biofilme verschlimmert werden? Cystic fibrosis.

data/lib/studium/exam_topics/bioinformatics

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+# =========================================================================== #
+# === BIOINFORMATICS tag
+#
+# Bioinf tag. Informatik Tag. Bioinfo tag. Bioinformatics Tag.
+# Also network-analysis.
+# =========================================================================== #
+
+- How do we call the <one>topmost node</one> in a tree? The <one>root node</one>. []
+- What do we mean with a <one>true tree</one> in bioinformatics? This is the tree that correctly reflects the history of our sequences used in (multiple) sequence alignment.
+- What means <one>identity</one> in bioinformatics? Identity describes the degree to which two or more sequnces are identical at each position.
+- Give a classical example of a <one>Bernoulli experiment</one>. A: The <one>(single) toss of a coin</one>. URL: https://en.wikipedia.org/wiki/Bernoulli_distribution []
+- Name a program that can be used in order to <one>identify repetitive elements in a genome</one>. A: <one>RepeatMasker</one>. URL: http://www.repeatmasker.org/ []
+- What is the <one>Burrows-Wheeler Transformation</one> (<one>BWT</one>)? This is a reversible permutation of the characters of a string, used originally for compression.
+- <one>FASTA</one> has <two>k-tuples values</two>. Which are the k values for DNA and protein? A: (1) <one>DNA</one>:     <two>k = 6</two> (2) <one>Protein</one>: <two>k = 2</two>
+- Name two methods that are commonly used in <one>structural genomics</one>. A: (1) <one>NMR</one> (2) <one>X-ray crystallography</one>
+- A. W. für <one>dotplot</one>? <one>2D-Matrix</one>. []
+- In <one>BLAST</one>: is it better to have a low or a high <two>E value</two>? The lower the E-value, or the closer it is to zero, the more "significant" the match is. So we ideally should like to have a <one>lower E value</one>.
+- In <peru>Bioinformatics</peru>: we assume that two sequences are homologous if ... ? If they are <two>derived</two> from a <one>common ancestor</one>. []
+- In phyologeny: <one>multifurcation</one> at a leaf means how many branches? At the least 3 branches. []
+- Give three different examples for <one>alphabets from biology</one>. A: (1) The Alphabet of <one>DNA nucleotides</one> (2) The Alphabet of <one>RNA nucleotides</one> (3) The Alphabet of the <one>20 amino acids</one> []
+- Wie unterscheidet sich die <one>deskriptive Statistik</one> von der <one>induktiven Statistik</one>? (1) Bei der "deskriptiven Statistik" beschreiben wir, wir sammeln, ordnen, fassen zusammen. (2) Bei der "induktiven Statistik" hingegen machen wir Schlussfolgerungen, Prognosen und basieren unsere Entscheidungen auf Wahrscheinlichkeiten.
+- What is the <one>FASTQ format</one>? This is like a FASTA file, but it also stores the <one>corresponding quality scores</one>. Very important for high-throughput machines such as Illumina Genome Sequencer.
+- <one>FASTQ</one> uses a <two>Quality score</two>. At <three>Q40</three> we can assume the sequence of a genome to be of high quality, and it may then be called ... ? A <one>reference genome</one>. []
+- Name a program that uses a "greedy algorithm" for nucleotide sequence alignment search. A: <one>Mega BLAST</one>.
+- In <one>applied bioinformatics</one>, we may see information obtained by <two>SRA</two>. What does <two>SRA</two> mean here? <one>Sequence read archives</one>. URL: https://www.ncbi.nlm.nih.gov/sra []
+- Was ist <one>DNA barcoding</one>? A taxonomic method that uses a "short genetic marker" in an organisms DNA to identify it as belonging to a particular species. It differs from "molecular phylogeny" in that the main goal is not to determine classification but to identify an unknown sample in terms of a known classification.
+- Wann wurde die Technik des <one>dynamischen Programmierens</one> eingeführt? <one>1953</one>. URL: https://de.wikipedia.org/wiki/Dynamische_Programmierung []
+- Archetypical example for "homologous proteins"? The <one>globin family of proteins</one>.
+- What match may we expect from a <one>decoy database</one>? <one>Not a true match</one>.
+- In der Bioinformatik: was bedeutet die Abkürzung "PSSM"? <one>Position Specific Scoring Matrix</one>.
+- In bioinformatics: what is the <one>most commonly used measure of similarity</one>? <one>Percent identity</one>. URL: https://en.wikipedia.org/wiki/Sequence_homology []
+- What is a <one>nr-database</one>? A <one>non-redundant database</one>. []
+- Das Programm <one>glimmer</one> benötigt Genomannotationen in welchem Format? Im <one>GFF Format</one> (<two>.gff</two>). []
+- In Bioinformatics: what are <one>variables</one>? These are <one>structures which can hold data</one>.
+- In Bioinformatics: why do we use <one>negative alignment scores</one> in residue pair alignments? This way we can "represent especially unlikely alignments".
+- Was ist eine <one>Metadatenbank</one>? Darstellung aller verfügbaren "biologischen" Datenbanken.
+- Why do we not use the <one>Smith-Waterman algorithm</one> for very large databases? Because <one>it would be way too slow</one>! []
+- Name one <one>SNP database</one>. A: The <one>public dbSNP database</one>. URL: https://en.wikipedia.org/wiki/DbSNP
+- Allgemein formuliert: wann verwenden wir die <one>Hamming distance</one>? Beim <one>Sequenzvergleich</one>.
+- In Bioinformatics: what do we usually mean with the Symbol S? This represents a string.
+- In BLAST: what does the name "E value" stand for? <one>Expect value</one>.
+- In der Bioinformatik: was heisst <one>NCBI</one>? <one>National Centre for Biotechnology Information</one>. URL: https://en.wikipedia.org/wiki/National_Center_for_Biotechnology_Information []
+- Was findet der <one>Needleman-Wunsch Algorithmus</one>? Er findet die minimale Distanz bei globalen paarweisen Alignments.
+- When we see a BLOSUM matrix with a high number, what can we infer from this? That this is a BLOSUM matrix designed for <one>comparing closely related sequences</one>.
+- <one>Quality scores</one> can be stored in FASTQ files. Typically there is the <three>Phred Score</three>. Would we prefer a high or low Phred score? A: A high one. It means <one>high accuracy</one>.
+- Why do we employ the <one>Nussinov algorithm</one>? We use this algorithm to <one>predict possible RNA secondary structure</one>.
+- What do we mean with <one>pairwise alignment</one> in bioinformatics? This is the process of lining up two sequences to achieve maximal levels of identity.
+- Why is <one>BLOSUM62</one> so widely used? Because it is fairly good at <one>detecting distant relationships</one> between proteins.
+- In <one>RNA Bioinformatics</one>: what do we mean with <two>hierarchical folding</two>? This is when the "secondary structure" forms first, and then helices arrange to form a <two>tertiary structure</two>.
+- Nenne mindestens drei wichtige Bioinformatikdatenbanken. A: (1) Protein Data Bank (PDB) (2) <one>GenBank</one> (3) PIR und Swiss-Prot
+- Give one example of a famous <one>nonredundant database</one>. A: <one>RefSeq</one>.
+- Name a <one>sequence graph</one> used in bioinformatics. A: The <one>De Bruijn</one> graph. URL: https://en.wikipedia.org/wiki/De_Bruijn_graph []
+- In the <one>Burrows-Wheeler Transformation</one>, we first have to generate all rotations, followed by ... ? Sorting them <one>lexicographically</one>.
+- <one>Pubmed</one> ist verfügbar seit ... ? <one>1966</one>. URL: https://de.wikipedia.org/wiki/PubMed []
+- The central bioinformatics institute in the USA is called <one>NCBI</one>. How do we call the similar institute in Europe? <one>EBI</one>. URL: https://en.wikipedia.org/wiki/European_Bioinformatics_Institute []
+- In a <one>Hidden Markov model</one>: what is meant with "silent states"? These are states that do not add to the sequence.
+- Anderes Wort für ein <one>Sequence Pattern</one>? A: <one>Motif</one>. []
+- In der <one>Bioinformatik</one>: wie heisst <two>die älteste Motivdatenbank</two>? <one>PROSITE</one>, <two>1988 erstellt</two>. []
+- In der Bioinformatik: wofür steht die Abkürzung "VEGA"? <one>Vertebrate Genome Annotation</one>.
+- Was erreicht man Dank der <one>SMART Datenbank</one> in der Bioinformatik? Eine Beschreibung von Proteindomänen.
+- Name <one>three example alphabets from biology</one>. A: (1) the <one>alphabet of DNA nucleotides</one> (2) the Alphabet of RNA nucleotides (3) the Alphabet of the 20 amino acids
+- From a bioinformatics point of view, how do we call <one>insertions</one> or deletions? A <one>gap in the alignment</one>.
+- If we see an entry such as <one>Q04679-2</one> in <two>UniProt</two>, what may the -2 indicate? This may refer to <one>Isoform 2</one>.
+- Entries in UniProtKB are uniquely identified by ... ? Their <one>accession number</one>.
+- The <one>main database containing protein sequences</one> together with their associated functional information is ... ? <one>UniProt</one>.
+- In Bioinformatics: what is the <one>Hamming distance</one>? Given two strings, the Hamming distance is the number of positions at which the corresponding symbols are different. In another way, it measures the minimum number of substitutions required to change one string into the other. Example: the Hamming distance between "toned" and "roses" is <one>3</one>.
+- In <one>DNA Barcoding</one> gibt es COI. Was heisst COI? mitochondrial cytochrome oxidase I gene.
+- Wann spricht man von einem <one>Laplace-Experiment</one>? Wenn <one>jedes Einzelereignis mit der selben Wahrscheinlichkeit auftreten kann</one>, wie zum Beispiel <two>bei einem Münzwurf</two> wo Kopf oder Zahl mit einer Wahrscheinlichkeit von 0.5 auftreten kann.
+- The plural form of a <one>taxon</one> is ... ? <one>Taxa</one>. []
+- An <one>oriented graph</one> in Bioinformatics has which two components? (1) a <one>start vertex</one> <two>bn</two> (2) an <one>end vertex</one> <two>en</two>
+- The <one>Blast k value</one> is normally <three>x for amino acids</three> and <three>y for nucleotides</three>. A: (1) 3-5 for aminoacids (2)  12 for nucleotides
+- In <one>gene ontology</one>: how do we technically describe "parentage"? Via <one>is_a</one> relationships.
+- Was ist ein <one>Mnemonic</one>? Ein Begriff der das Memorieren erleichtern soll.
+- How do we call the substring <one>S[1 . . . i]</one>? This is called the <one>prefix of S</one>.
+- <three>Which algorithm</three> is commonly used for <one>Maximum Parsimony</one>? The <one>Fitch's algorithm</one>. []
+- When is <one>GenBank</one> updated? <one>Every two months</one>. []
+- Das <one>Abschätzen der Wachstum einer Funktion</one> wird womit erreicht? Mit Hilfe der <one>O-Notation</one>. []
+- <one>Illumina Solexa</one> ist ein Paradebeispiel für die SBS Technologie. Was heisst SBS? <one>Sequencing by synthesis</one>. URL: https://emea.illumina.com/science/technology/next-generation-sequencing/sequencing-technology.html []
+- The <one>initial guide tree</one> that is created in progressive alignment methods, can be created by <three>efficient clustering methods</three>. Give two such examples. A: (1) <one>neighbor-joining</one> (2) <one>UPGMA</one>
+- The <one>Smith-Waterman algorithm</one> scores which 4 particular events? (1) <one>matches</one> (2) <one>mismatches</one> (3) <one>gaps</one> (4) <one>gap extensions</one>
+- What was the first commercial <one>single-molecule sequencer</one>? The <one>HeliScope</one>, by Helicos. URL: https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing
+- Welche Operationen sind bei der Kalkulation der Levenshtein-Distanz erlaubt (Antwort auf deutsch)? (1) <one>Einfügen</one> (2) <one>Löschen</one> (3) <one>Ersetzen</one>
+- Kann ein <one>progressives alignment</one> durch iterative Methoden verbessert werden? Ja. []
+- By comparing sequences through alignment, patterns of ... can be identified. A: Patterns of <one>conservation</one>.
+- Was heisst <one>homoplasy</one> wortwörtlich? <one>Selbe Form</one>.
+- <one>Unterschied</one> zwischen den primary databases und den secondary databases? A: Secondary databases sind curated, primary databases sind aus experimentellen Daten ohne <one>proofreading</one> entstanden. []
+- When can we say that two sequences are homologous? They are homologous if they are <one>derived</one> from a <two>common ancestor</two>.
+- In a <one>protein database</one>: what do we mean with "annotate"? This is all information other than the sequence.
+- Wann wurde die <one>Roche-454 Pyrosequenzierung</one> erfunden? <one>1996</one>. []
+- Was heisst <one>BLAST</one>? <one>Basic Local Alignment Search Tool</one>. URL: https://en.wikipedia.org/wiki/BLAST_(biotechnology) []
+- Which algorithm is faster: <one>Needleman-Wunsch</one> or <one>Smith-Waterman</one>? A: The <one>Needleman-Wunsch algorithm is faster</one>. (<two>needles are fast!</two>) []
+- <one>BLAST2</one>: why the 2 there? The <two>2</two> stands for the <one>Two-hit-method</one>.
+- <one>Progressive alignment</one> builds up a final MSA (Multiple Sequence Alignment). It starts with? It <one>starts with the similar pair</one> and progresses to the most distantly related one.
+- Was ist die kleinste Einheit in der Taxonomie? Das <one>Taxon</one>. []
+- What kind of algorithm is the <one>Baeza-Yates-Perleberg</one> algorithm? It is a <one>filtering algorithm</one>.
+- Say that a <one>dotplot</one> may show an <two>X-like area</two>. What can we conclude from this? There is <one>a palindrome in the sequence</one>. URL: http://www.globalspec.com/reference/65983/203279/the-dotplot []
+- In der Bioinformatik: angenommen wir möchten verschiedene Domänen darstellen. Was könnten wir hier verwenden? <one>psiBLAST</one>: <two>position specific interacted BLAST</two>
+- In Pseudocode: how to end a conditional <one>if</one>-statement? Via <one>end if</one>.
+- If we see pseudocode such as <one>s := s u 5</one>, what does this really mean, when the variable "s" is assumed to be a set? This <one>adds 5</one> to the set s; the <two>u</two> here stands for "union".
+- In the <one>UniProt Database</one>: how many of thse sequences are reliable and work at the cellular level as well? About <one>15% only</one>.
+- Wie nennt <one>PacBio</one> ihre <three>flowcell</three>? <one>Smart cell</one>. URL: https://www.pacb.com/smrt-science/smrt-sequencing/ []
+- In <one>FASTQ</one>: the <three>description line begins with which character</three>? <one>@</one>. []
+- Woher kommt der Name <one>RasMol</one>? Er kommt von <one>raster display of molecules</one>. []
+- Andere Bezeichnung für die <one>Distanz zwischen Zeichenfolgen</one>? <one>Hamming-Distanz</one>. []
+- In Sanger Sequencing: when <one>dye-terminator sequencing</one> is used, what exactly is fluorescently labeled? The <one>chain terminator ddNTPs</one> are fluorescently labeled.
+- What is a <one>clade</one>? A set of descendants from a single ancestor.
+- Based on their contents, <three>biological databases</three> can be roughly divided into which <one>three categories</one>? (1) <one>primary databases</one> (2) <one>secondary databases</one> (3) <one>specialized databases</one>
+- In Bioinformatics we have the <one>BAM files</one>. What does this stand for? <one>BAM</one> means <two>Binary Sequence Alignment</two>.
+- Was erlaubt einem die <one>O-Notation</one> in der Informatik? Ein Abschätzen des Wachstums einer Funktion.
+- In der Bioinformatik: warum sind <one>Bootstrapwerte</one> hilfreich? Sie <one>geben Auskunft darüber, wie konsistent der Datensatz ist</one>.
+- What can we do with the program <one>GRAIL</one>? We can <one>identify genes in a database</one>.
+- In <one>Gene Ontology</one>, one part also uses <two>evidence code</two>, assigned by automated methods. This automatically assigned evidence code comes from ...? It is <one>inferred from electronic annotation</one> (<two>IEA</two>).
+- Nenne einen <one>Algorithmus</one>, der als <three>Modell für Mutationsereignisse</three> dienen kann. A: Die <one>Maximum-likelihood Algorithmen</one>.
+- Name two different <one>amino acid substitution scoring matrices</one>. A: (1) <one>BLOSUM-62</one> (2) <one>PAM-120</one>
+- Give another name for a <one>rooted tree</one>. A: A <one>dendrogram</one>. []
+- In Bioinformatics or Statistics: what does <one>VCF</one> stand for? The <one>Variant Call Format</one>.
+- In Bioinformatics: why are <one>local alignments</one> often more reasonable than the Needleman-Wunsch agorithm? The Needleman-Wunsch algorithm often does not produce <one>biologically meaningful results</one>.
+- Nenne die 3 grössten, primären Sequenzatenbanken weltweit. A: (1) Genbank (2) EMBL (3) <one>DDBJ</one>
+- In der Bioinformatik: was sind die <one>OTUs</one>? Dies sind die <one>Operational Taxonomic Units</one>, relevant bei der Analyse von Stammbäumen (Phylogeny). URL: https://en.wikipedia.org/wiki/Operational_taxonomic_unit
+- If we have an <one>unrooted tree</one> with <three>4 elements</three>, how many rooted trees may we have? Show the formula for this as well. A: <two>5</two>. The formula is <one>(2n - 3)</one>, so (2 * 4 - 3) = 5. []
+- Seit wann ist der <one>Algorithmus zur Levenshtein-Distanz</one> bekannt? Seit <one>1965</one>. []
+- Give another word for <one>taxa</one>. A: <one>Operational taxonomic units</one>.
+- In Bioinformatics: <one>SRS</one> stands short for ... ? <one>Sequence retrieval system</one>.
+- What does a <one>Cladogram</one> show? It portrays the hierarchy of sister groupings between taxa, in a branching diagram.
+- In Bioinformatics: <one>TrEMBL</one> stands for ... ? <one>Translated EMBL</one>. URL: http://www.bioinfo.pte.hu/more/TrEMBL.htm []
+- Name a <one>multiple alignment program</one>. A: <one>ClustalW</one>. []
+- What are <one>heuristics</one>? <one>Fast algorithms</one> that aim to provide good solution in practice without guaranteeing the optimality or the near-optimality of the solution.
+- In <one>1997</one>: what was the upper limit of the database <two>GenBank</two>? (in KB) A: <one>350 kb</one>. []
+- <one>SRA size</one> is measured in ...bytes. A: <one>Petabytes</one>.
+- In bioinformatics: what is the bedtool <one>"-s"</one> option used for? <one>"-s"</one> stands here for <two>DNA strands</two>. Structural elements have to be on the same DNA strand, rather than the other strand.
+- Why the name <one>UniProt</one> for this database? <one>UniProt</one> stands for <two>universal protein database</two>. []
+- Consider you are given a <one>BLOSUM matrix</one> with very high numbers. What can this be used for? We can compare closely related sequences with a BLOSUM matrix with very high numbers. Low numbers are designed to compare distantly related sequences.
+- Explain this statement: <one>'Homology is a qualitative inference'</one>. A: This simply means that sequences are homologous - or they are not. []
+- Name <one>a substitution matrix</one> used for sequence alignment of proteins. A: <one>BLOSUM</one>. URL: https://en.wikipedia.org/wiki/BLOSUM []
+- In Bioinformatics, in the <one>Levensthein distance</one>: what means <three>Transposition</three> event? The <two>swapping</two> <one>of two characters</one>. []
+- <one>The first major bioinformatics project</one> was undertaken by <two>Margaret Dayhoff</two>, who developed a first protein sequence database called <three>Atlas of Protein Sequence and Structure</three>. In which year did this happen? In <one>1965</one>. []
+- How do we call the <one>default fragment length</one> in <two>FASTA</two>? <one>k-tup</one>. []
+- Why the name <one>dotplot</one>? Because in a dotplot, a <one>dot</one> is used to denote sequences that are similar.
+- In <one>ClustalW</one>, we speak about "once a gap, always a gap". What is meant with this? That <one>early mistakes are never corrected</one>.
+- In Bioinformatics: when we <one>make alignments</one>, what is <two>more costly</two>: a <three>mismatch</three> or a <three>gap</three>? <one>A gap should be more costly</one>. []
+- How can we define a <one>clade</one>? A clade is a group consisting of an ancestor and all its descendants, a single "branch" on the "tree of life".
+- What do we mean with the <one>biologically correct alignment</one>? This is <one>the alignment reflecting the true evolutionary history</one>.
+- A <two>FASTA file</two> may include <one>ASN.1</one>. This abbreviation stands for ... ? <one>Abstract Syntax Notation One</one>.
+- Name <one>a multiorganism genotype-phenotype database</one> that begins with the letter <three>P</three>. A: The <one>PhenomicDB database</one>.
+- When was the term <one>chemoinformatics</one> defined? In <one>1998</one>.
+- A <one>Markov chain</one> is traversed how? It is <one>traversed from state to state</one>, producing a <two>sequence of states</two>.
+- A <one>dotplot</one> in Bioinformatics shows an <three>X-like area</three>. What can we conclude from this? There is a <one>palindrome</one> in the given sequence. []
+- Name 3 different ways how <one>multiple sequence alignments</one> can happen. A: (1) progressive (2) iterative (3) blockwise
+- What are <one>exhaustive algorithms</one>? <one>Algorithms</one> that essentially <two>try all possible solutions</two>.
+- Give an example for <one>positive feedback</one> in biology. A: The conversion of Trypsinogen to Trypsin.
+- In Bioinformatics for a <one>suffix tree</one>, the character <three>$</three> is often used to terminate the given suffix tree. Why is <three>$</three> picked? Because <one>the terminal symbol may not be an existing character in the given string at hand</one>. []
+- The <one>Smith-Waterman algorithm</one> was improved in 1982 by Gotoh. That improvement came by handling ... what exactly? <one>Multiple sized gap penalties</one>.
+- Im <one>BLAST Interface</one> auf der NCBI Webpage, bei Proteinen, was ist der default? <one>BLOSUM62</one>. URL: https://www.ncbi.nlm.nih.gov/blast/html/sub_matrix.html []
+- Wir beobachten <one>unabhängige Vererbung</one>. Worauf deutet dies hin? Das verantwortliche Gene auf unterschiedlichen Chromosomen liegen.
+- Name the two main kinds of information inherent in any <one>phylogenetic tree</one>. A: (1) the <one>topology</one> (2) the <one>branch lengths</one>
+- Define the term <one>homoplasy</one>. A: <one>Structural resemblance</one> due to parallelism or <two>convergent evolution</two>, rather than to <two>common ancestry</two>.
+- Wie heisst der <one>Identifier</one> beim FASTA Format? A: <one>Accession Number.Version Number</one>.
+- When may we wish to use <one>PsiBLAST</one>? PsiBLAST is designed to be more sensitive than the original BLAST algorithm, so we may want to use it when we want to find "more distantly related proteins".
+- Name <one>a program</one> with which we could compare two (different) viral sequences. A: <one>MUMmer</one>. URL: https://mummer.sourceforge.net/ []
+- Andere Bezeichnung für <one>law of parsimony</one>? <one>Occam's razor</one>. URL: https://en.wikipedia.org/wiki/Occam%27s_razor []
+- If we define a word as <one>three letters</one>, which words can we find in the sequence <three>MGQLV</three>? (1) <one>MGQ</one> (2) <one>GQL</one> (3) <one>QLV</one> []
+- Was ist eine <one>binäre Antwort</one>? Eine <one>Ja</one>/<one>Nein Antwort</one>. []
+- Was ist der Unterschied zwischen einer <one>primary database</one> und einer <one>secondary database</one>? A: Eine Primäre Database ist die Rohfassung, eine Sekundäre Database ist die <one>curated</one> (also von anderen Leuten <one>gegengelesen</one>) []
+- Wie kann man einen <one>Dotplot</one> verbessern? Durch den <one>Einsatz von Filtern</one>. []
+- Francis Crick established the <one>central dogma</one>, which uses these common steps: gene → transcript → protein → phenotype. In the <two>NGS era</two>, we can translate this towards ... ? <one>genome</one> <two>→</two> <one>transcriptome</one> <two>→</two> <one>proteome</one> <two>→</two> <one>phenome</one> []
+- BRENDA was originally an acronym for ... ? The <one>Braunschweig Enzyme Database</one>. URL: https://en.wikipedia.org/wiki/BRENDA
+- <one>Molekulare Taxonomie</one> basiert auf ... ? <one>Sequenzen</one>.
+- Der <one>FASTA-Algorithmus</one> hat wieviele Phasen? <one>4</one>. []
+- Was bildet die Grundlage für das Quantifizieren der Sequenzähnlichkeit zwischen zwei Sequenzen? <one>Scores</one>.
+- In Bioinformatics, we have something such as <one>JC69</one>. What does this stand for? <one>Jukes Cantor model</one>. JC69 is the simplest substitution model. []
+- Eine <one>Substitutionsmatrix für den Vergleich von Aminosäurensequenzen</one> beruht auf welchem Prinzip? Auf der <one>chemischen Ähnlichkeit von Aminosäuren</one>.
+- What is <one>High-dimensional data</one>? That is data that requires more than two or three dimensions to represent.
+- What is a <one>substitution matrix</one> in bioinformatics? A substitution matrix describes the rate at which one character in a sequence changes to other character states over time.
+- Name <one>one drawback of GenBank</one>. A: GenBank is <one>highly redundant</one>.
+- What do we mean with a <one>reference genome</one>? This is a prototypic example that is representative of an entire species.
+- The <three>dynamic programming approach</three> can be extended for <one>multiple sequence alignment</one>. Give one example for that. A: Use a <one>multidimensional Needleman-Wunsch</one>, that is, a <two>(hyper)cube</two> instead of a matrix.
+- Name a simple mechanism for <one>generating scale-free networks</one>. A: "Preferential attachment" aka "the rich get richer".
+- Name one type of data that <one>GenBank</one> excludes. A: <one>Next-generation sequencing data</one>. []
+- Name 3 different types of <one>Phylogenetic Trees</one>. A: (1) cladogram (2) additive tree (3) <one>ultrametric tree</one>
+- Wie werden die <one>Strafpunkte</one> beim <two>globalen alignment</two> genannt? <one>Affine gap costs</one>. []
+- Was findet der <one>Needleman-Wunsch Algorithmus</one>? Er findet die <one>minimale Distanz bei globalen, paarweisen Alignments</one>.
+- <one>Starlight</one> uses ... to achieve <three>single-molecule sequencing</three>. A: <one>quantum dots</one>. []
+- In der Bioinformatik: zu welchem Zweck mögen wir eine <one>Dotplot-Analyse</one> einsetzen? Sie ist die einfachste Art und Weise wie wir <one>zwei verschiedene Sequenzen vergleichen</one> können.
+- Wofür steht <one>BLOSUM</one>? <one>BLOcks SUbstitution Matrix</one>.
+- Wofür steht das <peru>tr</peru> in <one>trEMBL</one>? <one>Translated</one>. []
+- In <one>Bioinformatics</one>: what do we mean with <two>ab initio methods</two>? These are methods that are helpful in order to determine new or rather unknown genes in a genome. It is a <one>gene prediction method</one>.
+- <one>ExPASy</one> stands for ...? <one>Expert Protein Analysis System</one>.
+- The <one>NCBI taxonomy database</one> contains over n registered organisms? Over <one>100_000</one> registered organisms.
+- In NGS, we have <one>SMRT sequencing</one>. This stands for ... ? <one>Single molecule real-time</one> sequencing.
+- The <one>PDB format</one> consists of lines of information in a text file. How do we call each line there? A <one>record</one>. []
+- The <one>Pfam database</one> classifies protein families according to <two>profiles</two>. What is meant with a profile in this context? A <one>profile</one> is a pattern that evaluates the probability of the appearance of a given amino acid, an insertion, or a deletion at every position in a protein sequence.
+- What is the name of the most famous <one>local alignment algorithm</one>? The <one>Smith-Waterman algorithm</one>.
+- Give 7 examples of <one>Main Applications of Phylogenies</one>. A: (1) Identification of organisms (bacteria, fungi, viruses) (2) Classification and taxonomy of genes, proteins and species (3) Comparative analysis and character evolution (4) Prediction of protein structure and function (5) Investigating the history and biology of populations (6) Studying the emergence and spread of viral and bacterial pandemics (7) Searching for useful traits in related groups
+- What are <one>NP-complete problems</one>? Problems which are equivalent - if a single problem in a set of thousand problems has a polynomial algorithm, all of them will have one.
+- The <one>post genomic era</one> allowed the formation of which science-division? <one>Proteomics</one>.
+- What means <one>UNA</one> in GenBank's data file entry? <one>Unannotated sequences</one>.
+- Was ist <three>schwieriger handzuhaben</three> in der Bioinformatik: <one>Globales Alignment</one> oder <one>Lokales Alignment</one>? <one>Globales Alignment</one>. Es umfasst ja auch mehr Nukleotide. []
+- Who hosts <one>GenBank</one>? <one>NCBI</one> does. []
+- In bioinformatics: what does the <one>jukes-cantor model</one> (JC69) assume? It assumes that the <one>equilibrium frequencies</one> of the four nucleotides are 25% each and that during evolution, any nucleotide has the same probability to be replaced by any other.
+- In Bioinformatics: what are <one>COGs</one>? <one>Clusters of Orthologous Genes</one> (COGs). These are defined groups of orthologous genes in various prokaryotic (COGs) and eukaryotic (KOGs) species. The COG database provides a functional and phylogenetic classification of protein groups based on "best-hit" blast results.
+- The path in the <one>Needleman and Wunsch algorithm</one> describes what? The <one>alignment of the (two) sequences</one>.
+- Name a software-tool for the identification of motifs. A: <one>COPIA</one>.
+- <one>Gene Ontology</one> uses which 3 ways to group genes together? (1) Where does a gene product act (2) What is the activity or "job" of a gene product, aka its "molecular function" (3) What is its "biological process" in the context of commonly recognized series of events, such as <one>limb development</one>
+- Is <one>homology</one> (in bioinformatics) measured in degrees? No - genes are either homologous or they are not. []
+- In <one>RNA bioinformatics</one>: does this domain focus more on sequence or on structure? RNA bioinformatics focuses more on (<one>RNA</one>) <one>structure</one>. []
+- In bioinformatics: how can we define an <one>edit distance</one>? The edit distance between two objects x and y is <one>the minimum number of operations</one> needed to convert x into y. []
+- When was the <one>Levenshtein distance</one> sequence alignment algorithm first suggested? In <one>1965</one>.
+- Name the 3 <one>principal genome browsers</one>. A: (1) Ensembl (2) UCSC (3) <one>NCBI</one>
+- In Bioinformatics: how is the <one>PAM</one> defined? <one>1 PAM</one> is <two>the time</two> for <one>1 substitution per 100 amino acids</one>.
+- The <one>PDB database</one> held how many structures in April 2020? <one>163141 structures</one>. []
+- Name a <one>major database for human disease</one>. A: <one>OMIM</one>. URL: https://www.omim.org/ []
+- Name the three general steps of the <one>Needleman-Wunsch approach</one>. A: (1) set up the matrix (2) score the matrix (3) identify the "optimal alignment"
+- What is the <one>key property of dynamic programming</one>? <one>Divide and conquer</one> - That a problem can be divided into many smaller parts.
+- Name a specific way in bioinformatics to search for protein sequences. A: <one>BLASTp</one>. URL: https://en.wikipedia.org/wiki/BLAST_(biotechnology) []
+- Is a <one>De Bruijn graph</one> a <three>multigraph</three>? Yes. []
+- If we see a file such as <one>cpg.bed</one>, where <peru>.bed</peru> stands for a <two>bedtools-related file</two>, what could this mean? The <one>cpg</one> could stand for <two>CpG islands</two> in a given genome, such as the human genome.
+- In bioinformatics: are <one>curated databases</one> considered to be <two>secondary databases</two>? Yes. []
+- In <one>Pseudocode</one>: how to do assignments? Via <one>:=</one> such as in <one>a := 5</one>. This would assign 5 to the variable a. []
+- When was <one>BLAST</one> first introduced? In <one>1989</one>.
+- What is the first <one>single-molecule sequencer</one>? <one>Helioscope</one>. URL: http://www.meragenome.com/how-it-works/technology
+- If two proteins are related at the sequence level, what does this imply? Relatedness of two proteins at the sequence level suggests that they are <one>homologous</one>.
+- <one>UniProt</one> stores protein sequences and their annotations where? In <one>UniProtKB</one>, also known as <one>the UniProt Knowledgebase</one>.
+- In der Genomik: wer oder liefert uns gute <one>Expressionsdaten</one>? <one>Microchips</one>.
+- What is <one>the key feature of Entrez</one>? Its ability to <one>integrate information</one>. This is very convenient: users do not have to visit multiple databases located in disparate places.
+- The <one>CAZy</one> database ... the CAZy stands for ... ? <one>Carbohydrate active enzyme database</one>.
+- Nenne einen wichtigen, wesentlichen Unterschied von KEGG zu anderen Datenbanken. A: KEGG besitzt eine deduktive Datenbank die es ermöglicht <one>Wirkdiagramme von Molekülen zu erstellen</one>.
+- Was sagt die <one>statistische Signifikanz</one> eines Experimentes aus? Sie sagt etwas über die Erklärbarkeit eines Resultats mit Hilfe des Zufalles aus.
+- What is a <one>Hamiltonian path</one>? This is a path that <one>visits each vertex exactly (and only) once</one>.
+- In general: how can the <one>Levenshtein distance</one> be computed? Via <one>dynamic programming</one>. []
+- <one>SCOP</one> (<two>Structural Classification Of Proteins</two>) classifies proteins of a known structure in a hierarchical manner. The three main classifications are ... ? (1) <one>families</one> (2) <one>superfamilies</one> (3) <one>folds</one>
+- Nenne zwei Methoden zur <one>Community Profiling</one>. A: (1) <one>DGGE</one> (2) <one>t-RFLP</one>
+- In bioinformatics: <one>SAM files</one> consist of two types of lines: <three>headers</three> and <three>alignments</three>. Headers begin with which character? <one>@</one>. []
+- The <one>third generation</one> of sequencing machines have which part in common? They all aim at <one>avoiding the amplification step</one>. []
+- What is an <one>ontology</one>? An "Ontology" is a formal representation of a set of concepts within a domain and the relationships between those concepts.
+- What is a <one>multiple sequence alignment</one>? This is when we <one>align more than 2 sequences</one>.
+- Was gilt beim <one>Occams Razor</one>? Es sollte bei "widersprüchlichen Modellen" stets das einfachere gewählt werden.
+- In Bioinformatics, what does S[i . . . j] mean? This is the contiguous substring of S that starts at position i, and ends including position j of S. []
+- How can we define <one>similarity</one> in bioinformatics? Similarity is a quantitative measure of how related two sequences are to one another.
+- Beschleunigt ein <one>guide tree</one> eine Berechnung? Ja. []
+- In Bioinformatics: what does <one>UPGMA</one> stand for? Unweighted Pair Group Method with Arithmetic Mean.
+- In bioinformatics: the "sum-of-pairs score, is used to assess ... ? <one>Multiple sequence alignments</one>.
+- <one>UniProt</one> versus <one>SwissPROT</one>: which of these two databases has a <three>higher quality</three>, on average? <one>SwissPROT</one>. []
+- What do we mean with <one>identity</one> in bioinformatics? This is the degree to which two or more sequences are actually <one>identical at each position</one>.
+- What kind of <one>PCR variant</one> is used in Roche/454-Pyrosequencing? An <one>emulsion PCR</one>.
+- In <one>Next-Generation Sequencing</one>: what do we have to do with the <three>raw sequencing reads</three>? We have to <one>align them towards a reference genome</one>.
+- Is the <one>Needleman-Wunsch algorithm</one> useful for database searches? No. []
+- <one>How many new species are added</one>, per month, into <one>GenBank</one>? <one>1000</one>.
+- How can we compare two sequences qualitatively? Via a <one>scoring system</one>.
+- The <one>SAM format</one>: what does SAM stand for? <one>Sequence Alignment</one>/<one>Map</one>.
+- Are <one>Transitions</one> more frequent than <one>Transversions</one>? Yes. []
+- Why do we not really make use of <one>exact string matching</one> for biological sequences? Because typically, two related biological sequences are not identical. Thus, approximate methods have to be used rather than exact ones.
+- In bioinformatics: can <one>literature databases</one> be classified as <two>secondary databases</two>? Yes. []
+- <one>KEGG</one> consists of how many different database? <one>16</one>.
+- What does a low E-value in <one>BLAST</one> mean? <one>This is good</one> - it indicates that the given match is very "significant".
+- What main assumption does UPGMA make? Sequences evolved at a <one>constant equal rate</one>.
+- In Bioinformatics: what is meant with <one>huge</one>? <one>Human genome equivalents</one>.
+- Nenne eine Datenbank, die sich dezidiert <one>Protein-Protein-Interaktionen</one> widmet. A: Die <one>STRING-Datenbank</one>.
+- Was bedeutet <one>maximum likelihood</one> in der Bioinformatik? Wir suchen den Baum der uns mit der größten Wahrscheinlichkeit unsere Daten generiert haben könnte.
+- The database <one>Pfam</one> stands for? <one>Protein families</one>. URL: https://en.wikipedia.org/wiki/Pfam []
+- What do we mean with the software <one>ApE</one>? This is <one>A plasmid Editor</one>.
+- Does a <one>contig</one> have gaps? No. []
+- In <one>pseudocode-expression</one>: how do we typically call an Array? We call an Array <one>a set of elements</one> such as <two>{1, 2, 3}</two>, without the " quotation marks.
+- Name the three steps in <one>dynamic programming</one>. A: (1) Initialization (2) Fill the matrix (3) <one>Traceback</one>
+- Die <one>wichtigste Datenbank für Proteinsequenzen</one> ist ... ? <one>UniProt</one>. URL: https://www.uniprot.org/ []
+- Why are <one>ESTs</one> useful in bioinformatics? Because they <one>indicate</one> - and help identify - <one>expressed genes</one>.
+- Andere Bezeichnung, ebenso auf Englisch, für <one>Parsimony</one>? <one>Minimum evolution</one>. []
+- Die <one>Bewertung des paarweisen Sequenzvergleichs</one> erfolgt mit Hilfe ...? Einer <one>Substitutionsmatrix</one>. []
+- Wann wurden <one>Hidden Markov Modelle</one> erstmals in der Bioinformatik eingesetzt? Im Jahre <one>1992</one>. []
+- The <one>JC69 model</one> is the simplest substitution model. Name the two main assumptions it does. A: (1) It assumes "equal base frequencies" (2) It assumes <one>equal mutation rates</one>
+- What are <one>extant species</one>? Exant species are <one>currently living species</one>. []
+- Beim <one>Log odds ratio</one> gibt es einen Bruch. Was steht im Zähler, was im Nenner? P(obs) / P(prior)
+- Give another term for the expression <one>None of the existing gaps are ever lost.</one>, in bioinformatics. A: <one>Once a gap, always a gap</one>. []
+- <one>ClustalW</one> creates what kind of tree? A <one>guide tree</one>.
+- In bioinformatics and phylogenesis: what means <one>multifurcation</one>? This is the occurrence of a split in an ancestral branch into more than two branches at an internal node.
+- What do we mean with <one>sequence alignment</one>? This is the comparison of different sequences, DNA or aminoacid, to detect <one>sequence similarity</one>.
+- From the point of view of bioinformatics: which problem may exist when we annotate a genome? Errors in a database can be continued and potentiated. This may lead to statements with a low information content such as "a putative protein is similar to another protein of unknown function that has unsubstantiated similarity to a protein kinase".
+- <one>Graphs</one> preserve ... relations. A: <one>neighborhood</one>.
+- In <one>pseudocode</one> used in bioinformatics: how do we denote a comment in that pseudocode? We will surround the comment in curly brackets, such as in <one>{a comment}</one>.
+- <one>Overrepresented sequences</one> in <two>FastQC</two> may indicate ... ? <one>Adapters</one>.
+- <three>Bioinformatic resources</three> come in which <one>two main flavors</one>? (1) <one>algorithms</one> (2) <one>databases</one>
+- Name <one>5 KEGG databases</one>. A: (1) KEGG PATHWAY (2) KEGG BRITE (3) KEGG MODULE (4) KEGG DISEASE (5) KEGG DRUG
+- From a bioinformatics point of view: why may <one>somatic change</one> be important to know about? Because it may be important in order to <one>study cancer</one>.
+- In bioinformatics: what does <one>XP</one> stand for in <one>XP_12345</one>? That these entries are <one>not based on experimental evidence</one>.
+- Name two different <one>substitution matrices</one> in Bioinformatics. A: (1) <one>BLOSUM</one> (2) <one>PAM</one> []
+- Was heisst <one>multifurcation</one> in der Bioinformatik? Das aus einem Ast mehr als zwei Äste entspringen.
+- What exactly do we mean with a <one>non-redundant</one> database in bioinformatics? Such a database, like <one>RefSeq</one>, will have identical sequences from the same organism and associated sequence fragments merged into a single entry.
+- Name <one>the most important format</one> used in <two>next-generation sequence analysis</two>. A: <one>FASTQ</one>. URL: https://en.wikipedia.org/wiki/FASTQ_format []
+- Die wichtigste Referenzdatenbank ist ... ? <one>PubMed</one>.
+- Which three actions could be performed should we wish to <one>calculate the edit distance</one> via the <two>Levensthein algorithm</two>? (1) Insert (2) <one>Delete</one> (3) <one>Replace</one>
+- How many entries did the <one>Protein Databank</one> (<two>PDB</two>) have in 1971 when it was just created? <one>7 entries</one>.
+- Why was the name <one>dynamic programming</one> chosen? The precise behaviour of the algorithm is established only when it runs, because it depends on the sequences being aligned.
+- Name the three main aspects of <one>genome sequencing</one>. A: (1) <one>Generate the sequence</one> (2) <one>Assembly</one> (3) <one>Annotation</one>
+- Is <three>BLAST</three> <one>local alignment</one> or <one>global alignment</one>? <one>Local alignment</one>.
+- <one>UniProt</one> is an abbreviation for ... ? <one>Universal Protein Resource</one>.
+- How many <one>degrees of homology</one> exist? There are <one>no degrees</one> - <two>sequences are either homologous or they are not</two>. []
+- In <peru>phylogeny</peru>: can there be <one>rooted trees</one> <two>without a known root</two>? Yes. []
+- Name a practical advantage of UNIX <one>text streams</one> in Bioinformatics. A: Text-Streams allow us to do processing on a "stream of data" rather than holding it all in memory.
+- Give a slightly longer name for <one>bioinformatics</one>. A: <one>Biological informatics</one>.
+- Which one contains more information: the <one>phylogram</one> or the <one>cladogram</one>? The "Phylogram". It provides the same information as a cladogram, though with the lengths of the branches made proportional to the number of characters transformations borne by them.
+- In Bioinformatics, for a <one>suffix tree</one>, every <three>internal node</three> has at least how many children? <one>Two</one>. []
+- Wann wurde die <one>Protein Data Bank</one> etabliert? Im Jahre <one>1971</one>.
+- Name a common pitfall that may lead to errors, in regards to <one>biological database</one>, if we tap into the information stored in these databases. A: There may be <one>many errors in sequence databases</one>. If such errors are passed to other databases it may lead to <two>a propagation of errors</two>.
+- Does a <one>rooted phylogenetic tree</one> or an <one>unrooted phylogenetic tree</one> contain more information? The <one>rooted phylogenetic tree</one> contains more information. []
+- The main barrier to linking different biological databases in bioinformatics is ... ? <one>Format incompatibility</one>.
+- A <one>hidden markov model</one> has a set of ... ? <one>States</one>.
+- What do we mean with <one>the Ontology of a database</one>? This is the list of valid terms and their definitions.
+- In der Bioinformatik: was versteht man unter <one>Edit distance</one>? Die <one>Edit Distance</one> ist die "Minimalanzahl an Operationen" (z.B. einfache Vertauschung), um Sequenz A in Sequenz B zu überführen.
+- In <one>bioinformatics</one>: give an example for <one>a prominent secondary database</one>. A: <one>SWISS-PROT</one>
+- In <one>metagenome sequence assembly</one> we follow the <three>ICARE</three> method. What does this stand for? (1) <one>Ignore</one> (2) Complement (3) Adapt (4) <one>Revise</one> (5) <one>Evaluate</one>
+- Current <one>biological databases</one> use which three types of database structures? (1) <one>flat files</one> (2) <one>relationa</one> (3) <one>object oriented</one>
+- How can <one>a phylogenetic tree</one> help us in general? It allows us to reconstruct evolutionary paths and thus help deduce functional conservatism.
+- <one>We can sequence whole genomes</one>. Name the 5 steps, starting from "sequence reads". A: (1) sequence reads (2) sequence contigs (3) scaffolds (4) mapped scaffolds (5) <one>genome map</one>
+- Provide one example for <one>sequencing by synthesis</one> and one example for <one>sequencing by ligation</one>. A: (1) <one>Sequencing by synthesis</one>: <two>Roche-454 Pyrosequencing</two>. (2) <one>Sequencing by ligation</one>:  <two>ABI SOLID</two>.
+- Nenne zwei Algorithmen die auf den <one>paarweisen Sequenzvergleich</one> setzen. A: (1) <one>Needleman-Wunsch Algorithm</one> (2) <one>Smith-Waterman Algorithm</one> []
+- Give an example for a <one>substitution matrix</one>. A: The <one>BLOSUM-62 substitution matrix</one>. URL: https://en.wikipedia.org/wiki/BLOSUM []
+- Wann wurde der <one>Smith-Waterman Algorithm</one> vorgeschlagen? <one>1981</one>.
+- Relevant for Bioinformatics, name the <one>correct classification for an organism</one>, as a chain. A: <one>Kingdom → Phylum → Class → Order → Family → Genus → Species</one> (<two>7</two>)
+- When was the <one>BLAST algorithm</one> developed? <one>1990</one>.
+- In Bioinformatics: what does the abbreviation <one>NGS</one> stand for? <one>Next Generation Sequencing</one>. []
+- Wann wurde <one>BLOSUM</one> entwickelt? <one>1992</one>.
+- When do we make use of <one>local alignment</one>? When we may have only one common domain.
+- In a <one>suffix array</one>: which character is typically the special <three>sentinel letter</three>? <one>$</one>. []
+- A. W. für <one>gap penalties</one>? <one>Affine gap costs</one>.
+- Wann wurden die <one>ESTs</one> eingeführt? A: <one>1993</one>. []
+- In Bioinformatics, what is a <one>contig</one>? This is a contiguous stretch of DNA sequence without gaps that has been assembled solely based on direct sequencing information.
+- How is a <one>clade</one> defined? A clade is a group consisting of an ancestor and all its descendants.
+- Der wichtigste Datenträger in der Molekularbiologie ist ... ? <one>DNA</one>. []
+- Are <one>negative scores</one> essential for local alignments? Yes. []
+- How does <one>FASTQ</one> extend <one>FASTA</one>? It includes <one>a numeric quality score</one> to each base in the sequence.
+- What exactly do we mean with <one>dynamic programming</one>? This is an algorithm that allows us to "find an optimal solution".
+- In Bioinformatics: what means <one>OTU</one>? <one>Operational taxonomic unit</one>. This is one of the organisms sequence-types being compared in a phylogenetic analysis, often represented by a DNA sequence or a biological pattern. []
+- Name a famous database accessible from <three>Entrez</three>, that contains <one>biomedical literature</one>. A: <one>PubMed</one>. []
+- In bioinformatics: when we use <one>a suffix tree</one>, how do we <two>terminate each substring</two>? We use the special character <peru>$</peru>. []
+- <one>Progressive alignment methods</one> in bioinformatics, have how many steps? <one>Two</one>. []
+- In der <one>Bioinformatik</one>: wann wurden <two>ESTs</two> eingeführt? <one>1993</one>; definiert wurde der Begriff aber bereits im Jahre <two>1991</two>. URL: https://en.wikipedia.org/wiki/Expressed_sequence_tag#History
+- What was the main idea behind <one>gap extension penalty</one>? That introducing a gap is a rare event, that extending a gap, however had, happens more regularly in biological systems.
+- Is <one>Parsimony</one> model-free? No, not really, even though this is often assumed. []
+- The <one>quality of bioinformatics predictions</one> depends on the sophistication of the algorithms being used and ... ? <one>the quality of the data</one>. 
+- What is <one>cladistics</one> all about? Identifying clades within clades from the distribution of characters inherited by resulting species.
+- <one>FASTQ</one> is typically used where? In <one>Next-Generation sequencing analysis</one>.
+- In <one>formal bioinformatics</one>: what does <one>|S|</one> indicate? <one>|S|</one> denotes <two>the length of a string S</two>. []
+- Why were the <one>BLOSUM matrices</one> developed? The goal was to replace the Dayhoff matrix with one that would perform best in identifying distant relationships.
+- How do we call the results derived from a <one>Levensthein-Distance</one>? <one>Alignment</one>.
+- What is a <one>gap penalty</one>? We need to penalize gaps in a sequence alignment.
+- We may see a new organism with lots of open reading frames (ORFs). Name a general way how we can infer which ORFs are really coding for proteins and which ones do not. A: An open reading frame that is not translated into protein usually contains all sense codons at about the same frequency, whereas the <one>reading frames that are translated into protein tend to use a subset of the codons</one>.
+- When may we wish to use <one>blastx</one>? When we wish to search protein databases using a translated nucleotide query.
+- Die Klassifikationseinheit ist in <one>SCOP</one> ...? Die <one>Proteindomäne</one>.
+- <one>The first bioinformatics database</one> was created by which person? <one>Margaret Dayhoff</one>. URL: https://en.wikipedia.org/wiki/Margaret_Oakley_Dayhoff []
+- In der Bioinformatik: nenne ein Beispiel für die <one>Poisson-Verteilung</one>. A: Das zufällige Auftreten einer Mutation in einer langen Sequenz.
+- We can use <one>special search terms in PubMed</one>. What does [AU] and [JID] mean, respectively? (1) <one>[AU]</one> will limit a search for the <two>author name</two> (2) <one>[JID]</one> will limit the search for a <two>journal name</two>
+- Name <one>a pioneer in Bioinformatics</one>. A: <one>Margaret Dayhoff</one>. []
+- The most commonly used score for MSAs is ... ? The <one>Sum of Pair Score</one>.
+- All major flatfiles in Bioinformatics include which 3 major parts? (1) The <one>header</one> (2) The <one>feature</one> (3) The <one>nucleotide sequence</one> itself
+- In <one>UPGMA</one>, how do we start? We build a <one>distance matrix</one> and start with the two most closely related sequences.
+- Warum wird das <one>Jukes & Cantor</one> Modell verwendet? Diese Methode wird verwendet, um Distanzdaten, die aus einem Sequenzalignment stammen, zu korrigieren.
+- How do we call the substring <one>S[j . . . |S|]</one>? This is called <one>suffix of S</one>. []
+- The term <one>bioinformatics</one> was coined in the year ... ? <one>1978</one>. []
+- In Bioinformatics: what is a <one>clade</one>? A monophyletic group of taxa sharing a closer common ancestry with one another than with members of any other clades.
+- In a <one>hidden markov model</one>: can a <two>transition</two> go directly back to the same state? Yes. []
+- In a <one>dotplot</one>: when will we use a dot? When the <one>two elements are equal</one>.
+- We have found a gene that may be responsible for a human disease. In which database shall we look first? In <one>OMIM</one> (<two>Online Mendelian Inheritance in Man</two>).
+- In bioinformatics: the <one>best-known genotype-phenotype database</one> is ... ? The <one>Online Mendelian Inheritance in Man (OMIM) database</one> of the NCBI.
+- The <one>FASTA-family</one> uses which BLOSUM by default? <one>BLOSUM50</one>. []
+- Name a database used in bioinformatics that makes use of <one>regular expressions</one>. A: <one>PROSITE</one>.
+- <one>UniRef</one> is a nonredundant sequence database that allows for fast similarity searches. The database exists in three versions: UniRef100, UniRef90, and UniRef50. What does UniRef50 mean here? This is a database that allows for the searching of sequences that are <one>≥50%</one> identical.
+- Bedeutet <one>BLOSUM50</one> <three>50% Ähnlichkeit zwischen zwei Sequenzen</three>? Ja. []
+- In der <one>PAM Substitutionsmatrix</one>: was eigentlich heisst <three>PAM</three>? <one>Percent Accepted Mutations</one>. (1 akzeptierte Punktmutation pro 100 Reste.) []
+- In bioinformatics: <one>query of the GenBank database</one> is carried out via ... ? The <one>NCBI Entrez system</one>.
+- In bioinformatics: the <one>GenBank entry</one> begins with which keyword normally, as a flat file? It begins with the keyword <one>LOCUS</one>, followed by a locus name.
+- In bioinformatics: sequences can be entered into GenBank by anyone via a Web page. How is this called? <one>bankit</one>. URL: https://www.ncbi.nlm.nih.gov/WebSub/
+- In bioinformatics: <one>primary databases</one> contain ... ? <one>Primary sequence information</one>, such as the nucleotide sequence or the protein sequence.
+- Nenne einen Nachteil der <one>primären Sequenzdatenbanken</one> in der Bioinformatik. A: <one>Fehlende Qualitätsprüfung</one>.
+- The first algorithm for comparing protein or DNA sequences was published by Needleman and Wunsch in ... which year? <one>1970</one>.
+- Who developed the <one>Entrez database</one>? The <one>NCBI</one>.
+- In der Bioinformatik: was ist eine <one>SP-Funktion</one>? <one>Sum-of-pair</one> Funktion.
+- Give another name for the term <one>Immunoinformatics</one>. A: <one>Computational immunology</one>.
+- Was ist die <one>feature table</one> bei der Annotation? Dieser Eintrag enthält Angaben zum Organismus, aus dem die DNA stammt.
+- How many genomes have been sequenced as of the year <one>2013</one>? About <one>3000</one>.
+- Wann wurde die <one>PROSITE Datenbank</one> erstellt? <one>1988</one>.
+- <one>Ab initio</one> gene discovery programs recognize such features to identify protein-coding genes. Most popular programs are based on ... ? <one>Hidden Markov Models</one> (<one>HMMs</one>).
+- Warum suchen wir in der Bioinformatik eigentlich nach <one>homologen Sequenzen</one>? Homologe Sequenzen implizieren in der Regel <one>eine ähnliche Funktion und Struktur</one>. []
+- Bei den <one>PacBio Sequencers</one>: nenne ein Problem ausser der "error rate". A: Die Geschwindigkeit beim Sequenzieren ist nicht konstant.
+- Name <one>two algorithms</one> that are based on <two>dynamic programming</two>. A: (1) the <one>Needleman-Wunsch algorithm</one> (2) the <one>Smith-Waterman algorithm</one> []
+- Nenne drei <one>boolesche Operatoren</one>. A: (1) <one>AND</one> (2) <one>OR</one> (3) <one>NOT</one>
+- What does the abbreviation <one>MIAME</one> stand for, in bioinformatics? <one>Minimum information about a microarray experiment</one>.
+- In Bioinformatics we may see SAM and BAM. How do these two relate to one another? BAM is essentially <one>compressed SAM</one>.
+- <one>IUPAC</one> uses the three letters B, D and H. These stand for ... ? (1) <one>B</one>: all bases except for <two>A</two>; <three>B</three> follows A (thus C, G, T) (2) <one>D</one>: all bases except for <two>C</two>; <three>D</three> follows C (thus A, G, T) (3) <one>H</one>: all bases except for <two>G</two>; <three>H</three> follows G (thus A, C, T)
+- <one>FASTQ</one> uses a <two>Quality score</two>, which starts at 0 and can go up to ... ? <one>40</one>.
+- A <one>FASTA file</one> contains which two parts, in general? (1) a <one>description</one> (2) the <one>sequence data</one>
+- When was <one>FASTA</one> introduced? In <one>1988</one>.
+- Who was the <one>predecessor</one> to <two>FASTA</two>? <one>FASTP</one>.
+- In <one>gene ontology</one> (GO), for proteins, we employ schemata that try to capture the entire complexity of protein functions. Name three different groups of GOs that are in use here, as a classification scheme. A: (1) molecular function (2) biological process (3) cellular component
+- Do we see <one>water molecules</one> in <two>RasMol</two>? No.
+- <one>Data splitting</one> in der Bioinformatik meint meistens ... ? Daten in subsets aufteilen und diese auf einem cluster zu parallelisieren.
+- What does <one>Ion Torrent</one> detect? It detects <one>hydrogen ions (H+)</one>.
+- In bioinformatics: why do we use a <one>dot plot</one>? The dot plot is a graphical method that allows the "comparison of two biological sequences".
+- <one>UPGMA</one> uses what kind of matrix? <one>UPGMA</one> uses a <two>distance matrix</two>.
+- The <one>Smith-Waterman algorithm</one> was first proposed by <two>Temple Smith</two> and <two>Michael Waterman</two> in what year? <one>1981</one>.
+- W. h. <one>Phi-Blast</one>? <one>Pattern-hit initiated BLAST</one>.
+- Name the 3 different <one>status levels</one> for <two>RefSeq</two>. A: (1) <one>predicted</one> (2) provisional (3) reviewed URL: https://www.ncbi.nlm.nih.gov/refseq/about/
+- Was sagt die <one>statistische Signifikanz</one> eines Experimentes aus? Sie sagt etwas über die Erklärbarkeit eines Resultats mit Hilfe des Zufalles aus.
+- Definiere in der Bioinformatik die <one>Hamming Distanz</one>. A: Dies ist <one>die Zahl der Austausche</one>, um von <two>Sequenz 1</two> zu <two>Sequenz 2</two> zu gelangen.
+- Bei der <one>KEGG database</one>: wofür steht <two>KEGG</two>? <one>Kyoto Encyclopedia of Genes and Genomes</one>.
+- What exactly is an <one>extant population</one>? This is <one>a population that is still existing</one>.
+- Name an <one>enzyme database</one>. A: <one>Brenda</one>. URL: http://www.brenda-enzymes.org
+- <one>DNA Barcoding</one> beruht auf welchem Verfahren? Auf der <one>Anwendung der Polymerase-Kettenreaktion</one> (<two>PCR</two>).
+- What is a <one>Phred quality score</one>? This is <one>a measure of the quality of the identification of the nucleobases</one> generated by <two>automated DNA sequencing</two>.
+- Wie geht die <one>Laplace-Formel</one>, erklärt? <one>Anzahl günstiger Ereignisse</one> dividiert durch die <two>Anzahl möglicher Ereignisse</two>.
+- Nenne die zwei zentralen Paradigmen/Schlagwörter in der Proteinevolution. A: (1) <one>Duplikation</one> (2) <one>Modifikation</one>
+- <one>Progressive alignment methods</one> represent the relationships between sequences in what form? As a <one>guide tree</one>.
+- In computer science we know of a <one>suffix tree</one>. Give another name for it. A: A <one>position tree</one>.
+- Das <one>FBI</one> verwendet <two>welche Datenbank</two> um genetische Spuren von möglichen Kriminellen zu identifizieren? <peru>CODIS</peru>: <one>Combined DNA Index System</one>.
+- In a <one>HMM</one> (<two>Hidden Markov Model</two>), transition between states has an assigned ...? <one>Probability</one>.
+- The <one>Hamming distance</one> considers only what? It considers only <one>point mutations</one>.
+- What is a <one>specialized database</one> in Bioinformatics? Also give an example for such a database, outside of the human species. A: A database that caters to a particular research interest, for instance: <one>Flybase</one>.
+- How much does it <one>cost</one> to sequence a human genome in the year 2015? About <one>$1000</one>.
+- In der Bioinformatik: was macht der <one>Smith-Waterman algorithm</one>? Er führt "local sequence alignments" durch. Das heisst er erkennt wie ähnlich zwei Strings zueinander sind.
+- What is the <one>ABI 3130xl</one>? A machine used to <one>automate Sanger sequencing</one>.
+- A. W. für <one>Backtracking</one> in der Bioinformatik? Ableiten des Alignments.
+- In order to achieve <one>maximum similarity</one> between two different sequences, of different length, we must do what? We must <one>introduce gaps</one>.
+- In der <peru>Bioinformatik</peru>: was heisst <one>PAM</one>? <one>Percent Accepted Mutation Matrix</one>.
+- Name a shortcoming of the <one>Sum of Pair Score</one>. A: It does not consider phylogeny.
+- What is the <one>holy grail of Bioinformatics</one>? The automatic construction of Metabolic Models from Sequenced Genomes.
+- Why would we wish to make use of <one>comparative genomics</one>? So that we can use a gene from one species, and find a related gene in another species.
+- In <one>ClustalW</one>: what does the <two>W</two> stand for? It stands for <one>weighted</one>.
+- Warum wird <one>blastx</one> verwendet? Da wir eine Nukleotidsequenz translatieren möchten, in allen möglichen Leserahmen - also sechs (<peru>6</peru>) Möglichkeiten in Summe.
+- Why are <one>different BLOSUM-matrices</one> used? Because they <one>can evaluate whether proteins are conserved to one another</one>. <two>BLOSUM62</two> can be used for <three>midrange evolution</three>, <two>BLOSUM80</two> can be used for <three>more related proteins</three> and <two>BLOSUM45</two> can be used for <three>distantly related proteins</three>.
+- What does the <one>law of parsimony</one> say? It states that <one>the simplest sufficient hypothesis</one> is to be preferred even though others are possible.
+- Name a <one>qualitative difference</one> between <two>PsiBLAST</two> and <two>BLAST</two>. A: PsiBLAST is more sensitive - it finds more distantly related sequences.
+- In bioinformatics, the <one>GFF</one> (<two>General Feature Format</two>) format consists of one line per feature, each containing n columns of data? <one>9 columns of data per line</one>.
+- Warum ist <one>Maximum-Parsimony</one> eigentlich <peru>minimal</peru>? Weil die Anzahl der Mutationen, die notwendig sind, um die evolutionäre Entwicklung zu erklären, minimal sein muss.
+- Eine <one>Substitutionsmatrix</one> für den Vergleich von Aminosäurensequenzen beruht auf welchem Prinzip? Es beruht auf dem Prinzip der <one>chemischen Ähnlichkeit von Aminosäuren</one>.
+- What feature does <one>dbEST</one> give its users? Access to <one>expressed sequence tags</one>.
+- Name a sequencing technique that requires a polymerase that is fixed to a surface. A: The <one>PacBio sequencing technique</one>.
+- <one>Gaps</one> in alignment, in bioinformatics, can be of which two types? (1) <one>internal</one> (2) <one>terminal</one>
+- In der Bioinformatik: wozu können wir <one>Hidden Markov Modelle</one> praktisch einsetzen? Zum <one>Detektieren von splice-Stellen</one>.
+- What do we mean with <one>Pseudocode</one> in bioinformatics? This is a language used by computer scientists to describe algorithms.
+- <one>PSI-BLAST</one> is a kind of <two>hybrid program</two> in between ... and ... ? (1) <one>BLAST</one> (2) <one>HMMs</one>
+- Was ist die elementare <one>Voraussetzung</one> für <two>Sequenzevolution</two>? <one>Mutationen</one>.
+- In <one>Bioinformatics</one>: what is meant with the term <one>RefSeq</one>? This is <one>the NCBI's Reference Sequences database</one>.
+- Name a <peru>constraint</peru> of the <one>Hamming distance</one>. A: It is <one>only applicable for sequences equal in length</one>.
+- Der <one>euklidische Abstand</one> ist ein Spezialfall der ...? <one>Minkonski Distanz</one>.
+- Give an example where <one>HMMs</one> have been used in bioinformatics, as an algorithm. A: <one>Gene-finding algorithms</one>.
+- What is <one>the most common bioinformatics task</one>? Given a query sequence, <one>find all similar sequences in a large database</one>.
+- Name two drawbacks of <one>ClustalW</one>. A: (1) Once a gap, always a gap (2) Guide tree bias
+- In order to determine the DNA sequence of an organism, two different methods have been very popular. Which ones? (1) The "ordered sequencing strategy", also called "clone contig method" (2) The "shotgun sequencing approach", with random processing of the fragments
+- When was the Protein databank (PDB) created? In "1971". (It was called "SEARCH" back then though).
+- How to do an assignment in pseudocode? For example via "a := 5".
+- What can we see as the "cancer hub" in human cells? The protein p53.
+- What is the main strength of a profile HMM? It is a "probabilistic model".
+- Name the three commonly used FASTQ quality schemes/scores in use. A: (1) <one>Sanger</one> (fastq-sanger) (2) "Solexa"   (fastq-solexa) (3) "Illumina" (fastq-illumina)
+- Wofür steht die "SCOP" Datenbank? "Structural classification of proteins".
+- Ist ein "Progressives Alignment" eine Heuristik? Ja.
+- What does the "Needleman-Wunsch algorithm" seek? It seeks the "optimal (global) alignment between two sequences".
+- Nenne ein "Antibiotikum", das durch metagenomische Forschung entdeckt wurde. A: "Turbomycin".
+- GOLD steht für ... ? "Genomes Online Database". URL: https://gold.jgi.doe.gov/
+- Name one solid reason why we may never be able to reconstruct the "true single tree of life". A: Because of the phenomenon of lateral gene transfer and gene loss, it might never be possible to construct a single tree of life that reflects the evolution of life on planet earth.
+- Die "Pfam-Datenbank" umasst 2008 etwa n Proteinfamilien? 10.340.
+- What do we mean with "Taxonomic novelty", in Bioinormatics? These are sequences without a close relative in a database.
+- Bioinformatic tools can be sequence-based or structure-based. Which variant is more powerful? The structure-based variant.
+- Nenne einen Algorithmus in der Bioinformatik, der mit "G" beginnt und sich mit Alignment von Sequenzen beschäftigt. A: Der "Gotoh-Algorithmus".
+- Give an example for "NGS to RNA". A: RNA-Seq.
+- How do "RefSeq" entries look like? For instance, NP_619745.1 URL: https://www.ncbi.nlm.nih.gov/protein/NP_619745.1
+- Nenne eine praktische Einsatzmöglichkeit eines Dotplots. A: Wenn man die Struktur zweier verschiedener Genome vergleichen möchte.
+- Why are there so many different BLOSUM matrices? Because there is no one correct scoring scheme for all circumstances.
+- What do we mean with "erroneous annotations" in Bioinformatics? The same gene sequence is found under different names, resulting in multiple entries and confusion about the data.
+- Was ist der Unterschied zwischen "primären" und "sekundären" Datenbanken? Sekundäre Datenbanken sind von primären Datenbanken abgeleitet. Primäre Datenbanken enthalten originale Information.
+- In Bioinformatics, what is a "superstring problem"? This is a problem where we have to find the shortest circular superstring that contains all possible k-mers as substrings.
+- A. W. für "Meta Databases"? Database on Databases.
+- In Bioinformatics, which two sets does a "graph" include? A graph includes a set of "vertices", and a set of "arcs".
+- When was the "dot plot" introduced in Bioinformatics? 1970, by Gibbs and McIntyre.
+- Nenne 1 Einschränkung bei der Hamming-Distanz. A: Es wird gleiche Sequenzlänge vorausgesetzt.
+- In Phylogenetic, internal nodes may also be called "HTU". What does the word HTU mean? Hypothetical taxonomic units. URL: http://en.wiktionary.org/wiki/hypothetical_taxonomic_unit
+- In der Bioinformatik, was ist allgemein ein "Alignment"? Das ist das Arrangieren von identischen oder ähnlichen Buchstaben zwischen mindestens 2 Sequenzen.
+- Was ist eine "Transversion"? Eine Veränderung Purin zu Pyrimidin oder umgekehrt.