@datagrok/bio 1.11.2 → 1.11.3
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package/README.md
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# Bio
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Bio is a [package](https://datagrok.ai/help/develop/develop#packages) for the
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Bio is a bioinformatics support [package](https://datagrok.ai/help/develop/develop#packages) for the
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[Datagrok](https://datagrok.ai) platform with an extensive toolset supporting SAR analisys for small molecules
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and antibodies.
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# Notations
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[@datagrok/bio](https://github.com/datagrok-ai/public/tree/master/packages/Bio) can ingest data in multiple file
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formats (such as fasta o csv) and multiple notations for natural and modified residues, aligned and non-aligned forms,
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nucleotide and amino acid sequences. The sequences are automatically detected and classified, while preserving their
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initial notation. Datagrok allows you to convert sequences between different notations as well.
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See:
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* [detectMacromolecule()](../Bio/detectors.js)
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* [class NotationConverter](../../libraries/bio/src/utils/notation-converter.ts)
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# Atomic-Level structures from sequences
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For linear sequences, the linear form (see the illustration below) of molecules is reproduced. This is useful
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for better visual inspection of sequence and duplex comparison. Structure at atomic level could be saved in available
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notations.
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You can easily run this feature for any sequence data using the Bio package and accessing it from the top menu.
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See:
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* [getMolfilesFromSeq()](./src/utils/atomic-works.ts)
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# MSA
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For multiple-sequence alignment, Datagrok uses the “kalign” that relies on Wu-Manber string-matching algorithm
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[Lassmann, Timo. _Kalign 3: multiple sequence alignment of large data sets._ **Bioinformatics** (2019).[pdf](
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https://academic.oup.com/bioinformatics/advance-article-pdf/doi/10.1093/bioinformatics/btz795/30314127/btz795.pdf)].
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“kalign“ is suited for sequences containing only natural monomers. Sequences of a particular column can be analyzed
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using MSA algorithm available at the top menu. Aligned sequences can be inspected for base composition
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at the position of MSA result.
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See:
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* [runKalign()](src/utils/multiple-sequence-alignment.ts)
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TODO: MSA with PepSeA
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# Splitting to monomers
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Splitting to monomers allows splitting aligned sequences in separate monomers.
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See:
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* [splitAlignedSequences()](../../libraries/bio/src/utils/splitter.ts)
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# Web Logo
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## Properties
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| Property name | Default
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| positionWidth | 16
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| minHeight | 50
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| maxHeight | 100
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| considerNullSequence | false
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| sequenceColumnName | null
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| startPositionName | null
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| endPositionName | null
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| Property name | Default | Description |
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|----------------------|----------|-------------------------------------------------------------------------------------------------------------------------|
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| positionWidth | 16 | Width of one position stack [px] |
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| minHeight | 50 | Minimum height of Logo [px] |
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| maxHeight | 100 | Maximum height of Logo [px] |
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| considerNullSequence | false | Should logo consider null seqences of data |
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| sequenceColumnName | null | source of multiple alignment sequences (column name) |
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| startPositionName | null | name of the first position to display Logo partially |
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| endPositionName | null | name of the last position to display Logo partially |
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| fixWidth | false | Plot takes full width required for sequence length |
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| verticalAlignment | 'middle' | choices: ['top', 'middle', 'bottom'] |
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| horizontalAlignment | 'center' | choices: ['left', 'center', 'right'] |
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| fitArea | true | Should control to be scaled to fit available area for viewer |
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| shrinkEmptyTail | true | Shrink sequences' tails empty in filtered sequences |
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| skipEmptyPositions | false | Skip positions containing only gap symbols in all sequences |
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| positionMarginState | 'auto' | choices: ['auto', 'enable', 'off'] Margin between positions. auto - enables margins for sequences of multichar monomers |
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| positionMargin | 0 or 4 | 4 - for sequences of multichar monomers, 0 - single char |
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| positionHeight | '100%' | choices: ['100%', 'Entropy'] The way to calculate overall monomers stack height at position |
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See also:
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* [
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* [
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* [WebLogo](../../libraries/)
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* [Viewers](../../help/visualize/viewers.md)
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* [Table view](../../help/datagrok/table-view.md)
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# Sequence space
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Datagrok allows visualizing multidimensional sequence space using a dimensionality reduction approach.
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Several distance-based dimensionality reduction algorithms are available, such as UMAP or t-SNE.
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The sequences are projected to 2D space closer if they correspond to similar structures, and farther
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otherwise. The tool for analyzing molecule collections is called 'Sequence space' and exists in
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the Bio package.
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To launch the analysis from the top menu, select Bio | Sequence space.
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See:
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* [sequenceSpace()](src/utils/sequence-space.ts)
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# Sequence activity cliffs
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Activity cliffs tool finds pairs of sequences where small changes in the sequence yield significant
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changes in activity or any other numerical property. open the tool from a top menu by selecting.
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Similarity cutoff and similarity metric are configurable. As in Sequence space, you can select
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from different dimensionality reduction algorithms.
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To launch the analysis from the top menu, select Bio | Sequence Activity Cliffs.
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See:
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* [getActivityCliffs()](../../libraries/ml/src/viewers/activity-cliffs.ts)
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