@datagrok/bio

Bio

Bio is a package for the Datagrok platform.

Web Logo

Web Logo is used to visualize a graphical representation of multiple sequence alignment (amino acids or nucleotides). Each logo consists of stacks of symbols, one stack for each position in the sequence. The overall height of the stack indicates the sequence conservation at that position, while the height of symbols within the stack indicates the relative frequency of each amino at that position.

In general, a sequence logo provides a richer and more precise description of, for example, a binding site, than would a consensus sequence.

You must specify the tag semType with value AminoacidsMultipleAlignment or NucleotidesMultipleAlignment for the data column with multiple alignment sequences, it is mandatory to select the palette for monomers' colors.

You can customize the look of the viewer with properties. Properties startPosition and endPosition) allow to display multiple alignment partially. If property startPosition (endPosition) is not specified, then the Logo will be plotted from the first (till the last) position of sequences.

General

Right click	Context menu

Properties

Property name	Default	Description
positionWidth	16	Width of one position stack [px]
minHeight	50	Minimum height of Logo [px]
maxHeight	100	Maximum height of Logo [px]
considerNullSequence	false	Should logo consider null seqences of data
sequenceColumnName	null	source of multiple alignment sequences (column name)
startPositionName	null	name of the first position to display Logo partially
endPositionName	null	name of the last position to display Logo partially

See also:

• Viewers
• Table view