Painting the alignment

Dear Jalview Team

I frequently need to highlight important residues/peptides into alignment. Your team had previously built a custom script for me to highlight a selection of peptide sequences onto an alignment (scrip attached). This script would take a list of peptides (from an input file which specifies peptide sequence, comment, required hex colour), find them into alignment and “paint” them with a specified colour.

I was wondering if you could help me tweak the script to similarly paint a list specified residues (from an input file which specifies sequence name, residue number, comment, required colour).

I am attaching the script, example alignment and the example input file.

Thank you for keeping Jalview so well-supported.

Best wishes

Manoj

aligned_cesa.fa (12.8 KB)

input.txt (577 Bytes)

(Attachment PeptidePainter1.groovy is missing)

Hello Manoj.

It sounds like you can just create a jalview feature file to do what you want.

Jalview’s help page: https://www.jalview.org/help/html/features/featuresFormat.html gives you a complete description, as well as a sample (at the end of the page). It allows you to create positional features on sequences by specifying their ID and the start and end of each feature, along with its type (which defines how it is coloured), and an accompanying description.

Thank you so much Jim. I will try your suggestion and come if any problems.

Best wishes

Manoj

Resending after changing the extension of .groovy file.

aligned_cesa.fa (12.8 KB)

input.txt (577 Bytes)

PeptidePainter1.txt (1.09 KB)