nightingale-colored-sequence

Use this component to paint a track that uses the sequence to paint a color depending on each residue.

Useful to display hydrophobicity, isoelectric points, or any feature where a color can represent a residue.

Usage

<nightingale-colored-sequence
  sequence="EXAMPLESEQUENCE"
  width="800"
  height="40"
  length="15"
  display-start="7"
  display-end="13"
  highlight="3:10"
  scale="hydrophobicity-scale"
></nightingale-colored-sequence>

API Reference

Properties

data: string

The sequence to use for the track. As an alternative to the sequence attribute inherited from nightingale-sequence

scale: string

The scale attribute is the mapping between a residue and a numeric value.

The value of this parameter could be either one of the predifined scales, or a custom scale indicating the values.

The list of predefined scales:

• hydrophobicity-scale
• hydrophobicity-interface-scale
• hydrophobicity-octanol-scale
• isoelectric-point-scale

The format for the custom scale is a comma separated list of pairs. Where each pair is a [KEY]:[VALUE]. For example:

A:0.5,M:-3,P:3

If a residue in the sequence is not defined in the used scale, the value used will be 0.

color-range: string

The color range attribute allow to define the colors to use when painting the values.

The component will use this range to create a scale that can be interpolated.

The default color_range is #ffdd00:-2,#0000FF:2 indicating that a value of -2 should be painted Yellow (#ffdd00) and a value of 2 should be blue (#0000FF). And values in between will be interpolated.

The format requires at least 2 points, and if more than 2 are given, the interpolation would be calculated in between segments. For example, #ffdd00:-2,white:0,#0000FF:2 where white is now representing the value0.

Notice that HTML color names are also supported, as in the example above.

Other attributes and parameters

This component inherits from NightingaleSequence.