@datagrok/bio 1.0.5 → 1.2.0
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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 [Datagrok](https://datagrok.ai) platform.
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# Web Logo
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Web Logo is used to visualize a graphical representation of multiple sequence alignment (amino acids or
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nucleotides). Each logo consists of stacks of symbols, one stack for each position in the sequence.
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The overall height of the stack indicates the sequence conservation at that position,
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while the height of symbols within the stack indicates the relative frequency of each amino at that position.
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In general, a sequence logo provides a richer and more precise description of, for example, a binding site,
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than would a consensus sequence.
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You must specify the tag ```semType``` with value ```AminoacidsMultipleAlignment``` or
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```NucleotidesMultipleAlignment``` for the data column with multiple alignment sequences, it is mandatory to
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select the palette for monomers' colors.
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You can customize the look of the viewer with properties. Properties ```startPosition``` and ```endPosition```)
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allow to display multiple alignment partially. If property ```startPosition``` (```endPosition```)
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is not specified, then the Logo will be plotted from the first (till the last) position of sequences.
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## General
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| | |
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|-------------|--------------|
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| Right click | Context menu |
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## Properties
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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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See also:
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* [Viewers](../viewers.md)
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* [Table view](../../overview/table-view.md)
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