studium 0.13.1

data/lib/studium/exam_topics/bioinformatics

@@ -0,0 +1,503 @@
+# =========================================================================== #
+# === BIOINFORMATICS tag
+#
+# Bioinf tag. Informatik Tag. Bioinfo tag. Bioinformatics Tag.
+# Also network-analysis.
+# =========================================================================== #
+
+- In bioinformatics we may see syntax such as <one>[1, 5)</one>. What does the [ and ) mean, respectively? This refers to a range. The [ means that it is included, so 1 is part of the range; the ) means that the last number, aka 5, is excluded, so it is not part of the range. Thus, the sequence here is: <two>1, 2, 3, 4</two>.
+- 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>)
+- The <one>NCBI taxonomy database</one> <two>contains over n registered organisms</two>? Over <one>100_000</one> registered organisms.
+- 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 <two>union</two>.
+- A <one>hidden markov model</one> has a set of ... ? <one>States</one>. []
+- <one>What kind of algorithm</one> is the <two>Baeza-Yates-Perleberg</two> algorithm? It is a <one>filtering algorithm</one>.
+- In bioinformatics: the <one>GenBank entry</one> <two>begins with which keyword</two> normally, as a flat file? It begins with the keyword <one>LOCUS</one>, followed by a locus name.
+- Name a program that uses a <one>greedy algorithm</one> for <two>nucleotide sequence alignment search</two>. A: <one>Mega BLAST</one>.
+- What does a low E-value in <one>BLAST</one> mean? <one>This is good</one> - it indicates that the given match is <two>very significant</two>.
+- An <one>oriented graph</one> in Bioinformatics has <two>which two components</two>? (1) a <one>start vertex</one> <two>bn</two> (2) an <one>end vertex</one> <two>en</two>
+- Name one drawback of the <one>dbEST</one> database. A: This database contains redundant ESTs, especially for strongly expressed genes such as actin.
+- What is the name of the database that <one>collects all EST data</one>? This is the <one>dbEST</one>.
+- The abbreviation <one>bl2seq</one> stands for ... ? <one>Blast two sequences</one>.
+- The database <one>Pfam</one> stands for? <one>Protein families</one>. URL: https://en.wikipedia.org/wiki/Pfam []
+- 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.
+- Die <one>Pfam-Datenbank</one> umfasste im Jahre <two>2008</two> etwa <three>n Proteinfamilien</three>? <one>10.340</one>. []
+- If we want to find out to which families a specific protein belongs to, which database should we consult? <one>InterPro</one>.
+- Give another name for <one>immunoinformatics</one>. A: <one>Computational immunology</one>.
+- <one>NCBI BLAST</one> uses <two>COBALT</two> (Papadopoulos and Agarwala 2007) to generate the multiple sequence alignment. What does <two>COBALT</two> stand for? <one>Constraint-based Multiple Alignment Tool</one>.
+- The most common strategy to compare two proteins involves ... ? <one>aligning their sequences</one>.
+- An individual <one>FASTQ record</one> must always contain ... how many lines? <one>4</one>.
+- The <one>Q</one> in <two>FASTQ</two> stands for ... ? <one>Quality</one>.
+- The computational methodology that tries to find the best matching between two molecule (such as a receptor and a ligand) is called ... ? Molecular docking.
+- The <one>Hamming distance</one> is basically equivalent in bioinformatics to ... ? SNPs: <two>single-nucleotide polymorphisms</two>.
+- What does the <one>Needleman-Wunsch algorithm</one> seek? It seeks the <one>optimal (global) alignment between two sequences</one>.
+- PAM matrices versus BLOSUM matrices: which one of these two is more often used for reconstructing phylogenetic trees? The <one>PAM matrices</one>.
+- What does <one>BLOSUM62</one>, that is the 62 there, indicate? BLOSUM62 indicates that the sequences selected for constructing the matrix share an average identity value of 62%.
+- We have found a gene that may be responsible for a human disease. In <one>which database</one> shall we look first? In <one>OMIM</one> (<two>Online Mendelian Inheritance in Man</two>). []
+- In Bioinformatics: what is meant with <one>huge</one>? <one>Human genome equivalents</one>. []
+- In Bioinformatics we may see <one>SAM</one> and <one>BAM</one>. How do these two relate to one another? <two>BAM</two> is essentially <one>compressed SAM</one>.
+- <one>Gene Ontology</one> uses <two>which three ways</two> to group genes together? (1) <one>Where</one> 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>
+- In Bioinformatics: why do we use <one>negative alignment scores</one> in residue pair alignments? This way we can <one>represent especially unlikely alignments</one>.
+- Give an example for an <one>empirical matrix</one> used in bioinformatics. A: The <one>BLOSUM matrices</one>.
+- <one>Welche Operationen</one> sind bei der Kalkulation der Levenshtein-Distanz erlaubt (Antwort auf deutsch)? (1) <one>Einfügen</one> (2) <one>Löschen</one> (3) <one>Ersetzen</one> []
+- Is <one>BLAST</one> a <two>heuristic algorithm</two>? Yes. []
+- In Bioinformatics: <one>SRS</one> stands short for ... ? <one>Sequence retrieval system</one>. []
+- Does the <one>Smith-Waterman algorithm</one> use <two>negative scores</two>? No. []
+- What kind of <one>PCR variant</one> is used in Roche/454-Pyrosequencing? An <one>emulsion PCR</one>. URL: https://pubmed.ncbi.nlm.nih.gov/26843044/ []
+- Are <one>SAM files</one> stored in <two>plain text</two>? Yes. []
+- 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 []
+- In bioinformatics: <one>query of the GenBank database</one> is carried out via ... ? The <one>NCBI Entrez system</one>. URL: https://www.ncbi.nlm.nih.gov/Web/Search/entrezfs.html []
+- The main barrier to linking different biological databases in bioinformatics is ... ? <one>Format incompatibility</one>. []
+- Bei den <one>PacBio Sequencers</one>: nenne ein Problem ausser der <two>error rate</two>. A: Die Geschwindigkeit beim Sequenzieren ist nicht konstant. []
+- In <one>BLAST</one>: is it better to have a low or a high <two>E value</two>? The lower the E-value, the more <one>significant</one> the match is. So we should ideally <one>prefer to have a very low lower E value</one>.
+- <one>UniProt</one> is an abbreviation for ... ? <one>Universal Protein Resource</one>. URL: https://en.wikipedia.org/wiki/UniProt
+- 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.
+- What exactly is an <one>extant population</one>? This is <one>a population that is still existing</one>. []
+- In <one>gene ontology</one> (<one>GO</one>), for proteins, we employ schemata that attempt to capture the entire complexity of protein functions. Name three different groups of <one>GOs</one> that are in use here, as a classification scheme. A: (1) <one>biological process</one> (2) <one>cellular component</one> (3) <one>molecular function</one>
+- 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>
+- What is a <one>gap penalty</one>? We need to penalize gaps in a sequence alignment.
+- Name <one>three example alphabets from biology</one>. A: (1) the <one>alphabet of DNA nucleotides</one> (2) the <one>alphabet of RNA nucleotides</one> (3) the <one>alphabet of the 20 amino acids</one> []
+- <one>How many new species are added</one>, per month, into <one>GenBank</one>? <one>1000</one>. []
+- How do we call the results derived from a <one>Levensthein-Distance</one>? <one>Alignment</one>. []
+- How can we compare two sequences qualitatively? Via a <one>scoring system</one>. []
+- Nenne eine <one>Einschränkung</one> bei der Hamming-Distanz. A: Es wird bei der Hamming-Distanz <one>gleiche Sequenzlänge vorausgesetzt</one>. []
+- Nenne ein "Antibiotikum", das durch metagenomische Forschung entdeckt wurde. A: <one>Turbomycin</one>.
+- When was the <one>Protein databank</one> (PDB) created? In <one>1971</one>. (It was called <two>SEARCH</two> back then though). []
+- Name two different <one>amino acid substitution scoring matrices</one>. A: (1) <one>BLOSUM-62</one> (2) <one>PAM-120</one> []
+- Was ist eine <one>Transversion</one>? Eine Veränderung Purin zu Pyrimidin oder umgekehrt. []
+- What is meant with the term <one>Taxonomic novelty</one>, in Bioinformatics? These are sequences without a close relative in a database.
+- Name a simple mechanism for <one>generating scale-free networks</one>. A: <one>Preferential attachment</one> aka <two>the rich get richer</two>.
+- Archetypical example for <one>homologous proteins</one>? The <one>globin family of proteins</one>. []
+- What is an <one>ontology</one>? An <one>Ontology</one> is a formal representation of a set of concepts within a domain and the relationships between those concepts.
+- <one>Overrepresented sequences</one> in <two>FastQC</two> may indicate ... ? <one>Adapters</one>. URL: https://www.bioinformatics.babraham.ac.uk/projects/fastqc/ []
+- <one>Molekulare Taxonomie</one> basiert auf ... ? <one>Sequenzen</one>. []
+- What do we mean with <one>pairwise alignment</one> in bioinformatics? This refers to <one>the process of lining up two sequences to achieve maximal levels of identity</one>.
+- <one>When</one> was <two>FASTA</two> introduced? In the year <one>1988</one>.
+- 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 der <one>Genomik</one>: wer oder was liefert uns gute <two>Expressionsdaten</two>? <one>Microchips</one>.
+- Wofür steht die "SCOP" Datenbank? <one>Structural classification of proteins</one>.
+- Nenne die <one>zwei zentralen Paradigmen</one>/</one>Schlagwörter</one> in der Proteinevolution. A: (1) <one>Duplikation</one> (2) <one>Modifikation</one>
+- Do we see <one>water molecules</one> in <two>RasMol</two>? No. []
+- In Bioinformatics: what is a <one>superstring problem</one>? This is a problem where we have to find the shortest circular superstring that contains all possible k-mers as substrings.
+- 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 []
+- Is <one>homology</one> quantifiable? No. Either two sequences are homologous - or they are not. []
+- When can we say that two sequences are homologous? They are homologous if they are <one>derived</one> from a <two>common ancestor</two>. []
+- The <one>Smith-Waterman algorithm</one> was improved in <two>1982</two> by Gotoh. That improvement came by handling ... what exactly? <one>Multiple sized gap penalties</one>.
+- What do we mean with <one>the Ontology of a database</one>? This is <one>the list of valid terms and their definitions</one>.
+- What is <one>the main strength of a profile HMM</one>? <one>HMM</one> is a <two>probabilistic model</two>.
+- Nenne mindestens <one>drei wichtige Bioinformatikdatenbanken</one>. A: (1) <one>Protein Data Bank</one> (<one>PDB</one>) (2) <one>GenBank</one> (3) <one>PIR</one> und <one>UniProt</one>
+- In der Bioinformatik: was versteht man unter <one>Edit distance</one>? Die <one>Edit Distance</one> ist die <two>Minimalanzahl an Operationen</two> (zum Beispiel durch einfache Vertauschung), um Sequenz A in Sequenz B zu überführen.
+- Wofür steht <one>BLOSUM</one>? <one>BLOcks SUbstitution Matrix</one>. URL: https://de.wikipedia.org/wiki/BLOSUM []
+- How does <one>FASTQ</one> extend <one>FASTA</one>? It includes <one>a numeric quality score</one> <two>to each base in the sequence</two>.
+- <one>Which three actions</one> could be performed should we wish to <two>calculate the edit distance</two> via the <three>Levensthein algorithm</three>? (1) <one>Insert</one> (2) <one>Delete</one> (3) <one>Replace</one> []
+- <one>When</one> may we wish to use <two>PsiBLAST</two>? <one>PsiBLAST</one> is designed to be more sensitive than the original BLAST algorithm, so we may want to use it when we want to find <two>more distantly related proteins</two>.
+- A. W. für <one>Backtracking</one> in der Bioinformatik? <one>Ableiten des Alignments</one>.
+- What <one>main assumption</one> does <two>UPGMA</two> make? <one>UPGMA</one> assumes that sequences have evolved at a <two>constant equal rate</two>.
+- In a <one>protein database</one>: what do we mean with <two>annotate</two>? This is all information other than the sequence.
+- <one>Bioinformatic tools</one> can be sequence-based or structure-based. Which variant is more powerful? The <one>structure-based variant</one>. []
+- Name a practical advantage of UNIX <one>text streams</one> in Bioinformatics. A: Text-Streams allow us to do processing on a <one>stream of data</one> rather than holding it all in memory.
+- How to do an assignment in pseudocode? For example via <one>a := 5</one>. []
+- The <one>main database containing protein sequences</one> together with their associated functional information is ... ? <one>UniProt</one>. URL: https://en.wikipedia.org/wiki/UniProt []
+- Name <one>a sequencing technique</one> that requires a polymerase that is fixed to a surface. A: The <one>PacBio sequencing technique</one>.
+- <one>ClustalW</one> creates what kind of tree? A <one>guide tree</one>. URL: https://www.biostars.org/p/70676/ []
+- <one>Progressive alignment methods</one> represent the relationships between sequences in what form? As a <one>guide 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>. URL: https://en.wikipedia.org/wiki/Combined_DNA_Index_System []
+- <one>GOLD</one> steht für ... ? <one>Genomes OnLine Database</one>. URL: https://gold.jgi.doe.gov/
+- When was <one>BLAST</one> first introduced? In <one>1989</one>. URL: https://en.wikipedia.org/wiki/BLAST_(biotechnology) []
+- 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> []
+- <one>ClustalW</one> was subsequently superseded by ... ? <one>Clustal Omega</one>.
+- Was ist der Unterschied zwischen <one>primären</one> und "sekundären" Datenbanken? Sekundäre Datenbanken sind von primären Datenbanken abgeleitet. Primäre Datenbanken enthalten originale Information.
+- In bioinformatics: two protein sequences can be regarded as <one>homologous</one> if the percentage sequence identity falls in the ... ? <one>safe zone</one>.
+- <one>Wann</one> wurde die <two>Protein Data Bank</two> etabliert? Im Jahre <one>1971</one>.
+- Nenne die drei grössten, primären Sequenzatenbanken weltweit. A: (1) <one>Genbank</one> (2) <one>EMBL</one> (3) <one>DDBJ</one>
+- In a <one>Hidden Markov model</one>: what is meant with <two>silent states</two>? These are states that do not add to the sequence.
+- In bioinformatics: <one>Scoring matrices</one> allow the computation of ... ? <one>optimal alignments</one>.
+- In bioinformatics: the <one>sum-of-pairs score</one>, is used to assess ... ? <one>Multiple sequence alignments</one>.
+- Which one contains more information: the <one>phylogram</one> or the <one>cladogram</one>? The <one>Phylogram</one>. 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.
+- Name one solid reason why we may never be able to reconstruct the <one>true single tree of life</one>. 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.
+- Nenne eine <two>Datenbank</two>, die sich dezidiert <one>Protein-Protein-Interaktionen</one> widmet. A: Die <one>STRING-Datenbank</one>.
+- Ist ein <one>Progressives Alignment</one> eine <two>Heuristik</two>? Ja. []
+- 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 do we mean with a <one>reference genome</one>? This is <one>a prototypic example that is representative of an entire species</one>.
+- Name a <peru>constraint</peru> of the <one>Hamming distance</one>. A: The <two>Hamming distance</two> is <one>only applicable for sequences equal in length</one>. []
+- Nenne drei <one>bool'schen Operatoren</one>. A: (1) <one>AND</one> (2) <one>OR</one> (3) <one>NOT</one> []
+- What are <one>exhaustive algorithms</one>? These are <one>algorithms</one> that essentially <two>try all possible solutions</two>.
+- In Bioinformatics: what do we usually mean with the <one>Symbol S</one>? This represents a string. []
+- 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>.
+- <one>Parallel diagonal lines</one> within a dot-plot matrix represent ...? <one>Repetitive regions of the sequences</one>.
+- What was the first <one>single-molecule sequencer</one>? <one>Helioscope</one>. URL: https://en.wikipedia.org/wiki/Helicos_single_molecule_fluorescent_sequencing
+- The most basic sequence alignment method is ... ? The <one>dot matrix method</one>, as can be seen in a <two>dot plot</two>.
+- In a given .pdb file, what is the <one>centroid</one> of a structure? This is <one>the average position of the atoms</one>.
+- Wir beobachten <one>unabhängige Vererbung</one>. Worauf deutet dies hin? Das verantwortliche Gene auf unterschiedlichen Chromosomen vorzufinden sind. []
+- Was heisst <one>Phi-Blast</one>? <one>Pattern-hit initiated BLAST</one>.
+- How do we call the substring <one>S[1 . . . i]</one>? This is called the <one>prefix of S</one>. []
+- Name the three general steps of the <one>Needleman-Wunsch approach</one>. A: (1) set up the matrix (2) score the matrix (3) <one>identify</one> the <two>optimal alignment</two>
+- When we see a <one>BLOSUM matrix</one> with a high number, what can we infer from this? That this is a <two>BLOSUM matrix</two> designed for <one>comparing closely related sequences</one>.
+- We can distinguish between global alignment and local alignment when doing sequence alignment. One of these two alignment strategies assumes that the two sequences have similarity over their entire length. Which one of these two does assume this? <one>Global alignment</one>.
+- Simply put: <one>the overall goal of pairwise sequence alignment is ... </one>? <one>To find the best pairing of two sequences, such that there is maximum correspondence among residues</one>.
+- Name an <one>enzyme database</one>. A: <one>Brenda</one>. URL: https://www.brenda-enzymes.org/ []
+- In der Bioinformatik: was macht der <one>Smith-Waterman algorithm</one>? Er führt <two>local sequence alignments</two> durch. Das heisst er erkennt wie ähnlich zwei Strings zueinander sind.
+- <one>IUPAC</one> uses the three letters <two>B</two>, 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)
+- Current <one>biological databases</one> use which three types of database structures? (1) <one>flat files</one> (2) <one>relational</one> (3) <one>object oriented</one>
+- In Bioinformatics: what is the <one>Hamming distance</one>? Given two strings, <two>the Hamming distance is the number of positions at which the corresponding symbols are different</two>. In another way, the Hamming distance 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>.
+- Name the three commonly used <one>FASTQ quality schemes</one>/<one>scores</one> in use. A: (1) <one>Sanger</one> (fastq-sanger) (2) <one>Solexa</one>   (fastq-solexa) (3) <one>Illumina</one> (<two>fastq-illumina</two>)
+- In der Bioinformatik: was sind die <one>OTUs</one>? Dies sind die <one>Operational Taxonomic Units</one>, <two>relevant bei der Analyse von Stammbäumen</two> (<three>Phylogeny</three>). URL: https://en.wikipedia.org/wiki/Operational_taxonomic_unit
+- In <one>gene ontology</one>: how do we technically describe <two>parentage</two>? Via <one>is_a</one> relationships.
+- When was the <one>dot plot</one> introduced in Bioinformatics? <one>1970</one>, by Gibbs and McIntyre.
+- <one>SRA size</one> is measured in ... bytes. A: <one>Petabytes</one>.
+- In the <one>UniProt Database</one>: how many of these sequences, in percent, are reliable and work at the cellular level as well? About <one>15% only</one>.
+- In order to determine the DNA sequence of an organism, two different methods have been very popular. Which ones? (1) The <one>ordered sequencing strategy</one>, also called "clone contig method" (2) The "shotgun sequencing approach", with random processing of the fragments
+- In Bioinformatics: which two sets does a <one>graph</one> include? A graph includes a set of "vertices", and a set of "arcs".
+- Die <one>wichtigste Referenzdatenbank</one> ist ... ? <one>PubMed</one>.
+- The <one>most commonly used score for MSAs</one> is ... ? The <one>Sum of Pair Score</one>.
+- How many entries did the <one>Protein Databank</one> (<two>PDB</two>) have in 1971 when it was just created? Only <one>7 entries</one>.
+- What exactly do we mean with <one>dynamic programming</one>? This is an algorithm that allows us to <one>find an optimal solution</one>.
+- In der Bioinformatik: was bedeutet die Abkürzung <one>PSSM</one>? <one>Position Specific Scoring Matrix</one>.
+- <two>Warum</two> wird das <one>Jukes & Cantor</one> Modell verwendet? Diese Methode wird verwendet, um Distanzdaten, die aus einem Sequenzalignment stammen, zu korrigieren.
+- Nenne einen wichtigen, wesentlichen Unterschied von KEGG zu anderen Datenbanken. A: <two>KEGG</two> besitzt eine deduktive Datenbank die es ermöglicht <one>Wirkdiagramme von Molekülen zu erstellen</one>.
+- Name <one>one drawback of GenBank</one>. A: <two>GenBank</two> is <one>highly redundant</one>.
+- Give another name for <one>Meta Databases</one>. A: <one>Database on Databases</one>. []
+- Was gilt beim <one>Occams Razor</one>? Es sollte bei <one>widersprüchlichen Modellen</one> stets das einfachere gewählt werden.
+- <one>We can sequence whole genomes</one>. Name the 5 steps, starting from <two>sequence reads</two>. A: (1) sequence reads (2) sequence contigs (3) scaffolds (4) <one>mapped scaffolds</one> (5) <one>genome map</one>
+- Entries in <one>UniProtKB</one> are uniquely identified by ... ? Their <one>accession number</one>.
+- Eine <one>Substitutionsmatrix für den Vergleich von Aminosäurensequenzen</one> beruht auf welchem Prinzip? Auf der <one>chemischen Ähnlichkeit von Aminosäuren</one>. []
+- In bioinformatics: why do we use a <one>dot plot</one>? The dot plot is a graphical method that allows the <one>comparison of two biological sequences</one>.
+- Give an example for <one>NGS to RNA</one>. A: <one>RNA-Seq</one>. URL: https://en.wikipedia.org/wiki/RNA-Seq []
+- Was erlaubt einem die <one>O-Notation</one> in der Informatik? Ein <one>Abschätzen des Wachstums einer Funktion</one>.
+- <one>BRENDA</one> was originally an acronym for ... ? The <one>Braunschweig Enzyme Database</one>. URL: https://en.wikipedia.org/wiki/BRENDA
+- Nenne einen Algorithmus in der Bioinformatik, der mit dem Buchstaben <one>G</one> beginnt und sich mit Alignment von Sequenzen beschäftigt. A: Der <one>Gotoh-Algorithmus</one>. URL: https://de.wikipedia.org/wiki/Gotoh-Algorithmus []
+- In Phylogenetics: internal nodes may also be called <one>HTU</one>. What does the word <one>HTU</one> mean? <one>Hypothetical taxonomic units</one>. URL: https://en.wiktionary.org/wiki/hypothetical_taxonomic_unit []
+- Is <three>BLAST</three> <one>local alignment</one> or <one>global alignment</one>? <one>Local alignment</one>. []
+- All <one>major flatfiles</one> in Bioinformatics include which 3 major parts? (1) The <one>header</one> (2) The <one>feature</one> (3) The <one>nucleotide sequence</one> itself
+- What does <one>Ion Torrent</one> detect? It detects <one>hydrogen ions (H⁺)</one>.
+- When was the term <one>chemoinformatics</one> defined? In the year <one>1998</one>. []
+- What can we see as the <one>cancer hub</one> in human cells? The protein <one>p53</one>.
+- In Pseudocode: <two>how to end</two> a conditional <one>if</one>-statement? Via <one>end if</one>.
+- From a bioinformatics point of view: how do we call <one>insertions</one> or <one>deletions</one>? A <one>gap in the alignment</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 <two>high one</two>. It means <one>high accuracy</one>.
+- The golden rule of applied bioinformatics is ... ? To not trust your tools or data.
+- 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 <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>. []
+- 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 []
+- What match may we expect from a <one>decoy database</one>? <one>Not a true match</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>.
+- 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 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.
+- Why do we employ the <one>Nussinov algorithm</one>? We use this algorithm to <one>predict possible RNA secondary structure</one>.
+- 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>.
+- 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 []
+- 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.
+- 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>.
+- 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>. []
+- 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
+- Was ist ein <one>Mnemonic</one>? Ein Begriff der das Memorieren erleichtern soll.
+- <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>
+- 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. []
+- 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>. []
+- 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>
+- 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>.
+- 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>.
+- 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>.
+- 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>.
+- 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>. []
+- 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>.
+- 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
+- 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>. []
+- 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 []
+- 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>.
+- 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> []
+- 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. []
+- 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.
+- 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 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 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>.
+- 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>. []
+- 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>.
+- 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/ []
+- 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. []
+- 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>.
+- 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>.
+- 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 a <one>multiple sequence alignment</one>? This is when we <one>align more than 2 sequences</one>.
+- 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.
+- <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>.
+- 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. []
+- 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>.
+- Was bedeutet <one>maximum likelihood</one> in der Bioinformatik? Wir suchen den Baum der uns mit der größten Wahrscheinlichkeit unsere Daten generiert haben könnte.
+- 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. []
+- 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>. []
+- 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>.
+- <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 []
+- 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>
+- 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. []
+- Give a slightly longer name for <one>bioinformatics</one>. A: <one>Biological informatics</one>.
+- In Bioinformatics, for a <one>suffix tree</one>, every <three>internal node</three> has at least how many children? <one>Two</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. []
+- 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>
+- How can <one>a phylogenetic tree</one> help us in general? It allows us to reconstruct evolutionary paths and thus help deduce functional conservatism.
+- 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>.
+- 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>$</one>. []
+- A. W. für <one>gap penalties</one>? <one>Affine gap costs</one>.
+- Wann wurden die <one>ESTs</one> eingeführt? A: <one>1993</one>. []
+- How is a <one>clade</one> defined? A clade is a group consisting of an ancestor and all its descendants.
+- Der wichtigste Datenträger in der Molekularbiologie ist ... ? <one>DNA</one>. []
+- Are <one>negative scores</one> essential for local alignments? Yes. []
+- In Bioinformatics: what means <one>OTU</one>? <one>Operational taxonomic unit</one>. This is one of the organisms sequence-types being compared in a phylogenetic analysis, often represented by a DNA sequence or a biological pattern. []
+- Name a famous database accessible from <three>Entrez</three>, that contains <one>biomedical literature</one>. A: <one>PubMed</one>. []
+- In bioinformatics: when we use <one>a suffix tree</one>, how do we <two>terminate each substring</two>? We use the special character <peru>$</peru>. []
+- <one>Progressive alignment methods</one> in bioinformatics, have how many steps? <one>Two</one>. []
+- 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.
+- 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.
+- Name <one>a pioneer in Bioinformatics</one>. A: <one>Margaret Dayhoff</one>. []
+- In <one>UPGMA</one>, how do we start? We build a <one>distance matrix</one> and start with the two most closely related sequences.
+- 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>.
+- 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>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>. []
+- 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> []
+- What does the abbreviation <one>MIAME</one> stand for, in bioinformatics? <one>Minimum information about a microarray experiment</one>.
+- <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>
+- Who was the <one>predecessor</one> to <two>FASTA</two>? <one>FASTP</one>.
+- <one>Data splitting</one> in der Bioinformatik meint meistens ... ? Daten in subsets aufteilen und diese auf einem cluster zu parallelisieren.
+- <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>.
+- 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>.
+- <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>.
+- In computer science we know of a <one>suffix tree</one>. Give another name for it. A: A <one>position tree</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>.
+- What is the <one>ABI 3130xl</one>? A machine used to <one>automate Sanger sequencing</one>.
+- 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.
+- What feature does <one>dbEST</one> give its users? Access to <one>expressed sequence tags</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>.
+- 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
+- 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.
+- In der Bioinformatik, was ist allgemein ein "Alignment"? Das ist das Arrangieren von identischen oder ähnlichen Buchstaben zwischen mindestens 2 Sequenzen.