Single Position Highlight In Multiple Sequence Alignment

Question

[Kamila001]

Hi All,

I have multiple sequence alignments of homologous species of more than 1000 proteins in .aln format. For each protein, i have an interested amino acid position for dogs.I am interested in highlighting that position in the alignment. One obvious way is to use Jalview using tool like MUSCLE and highlight it manually one by one. Is there any script or code that can do this? Any suggestions would be usefull.

[Neilfws]

"Homologous" means "similar due to shared ancestry". I don't think you should say "homologous species".

[Kamila001]

true … its homologous sequences i guess?

[Kamila001]

True… its homologous sequences i guess

Answer 1

[DG]

Jalview has an annotation track that can be output as text to appropriate alignment files. So your best bet is to bust out your favourite scripting language and use it to write the annotations into the alignment files. Here is the link to the documentation for Jalview annotation files. You should be able to create one in a scripting pipeline easily enough.

http://www.jalview.org/help/html/features/annotationsFormat.html

[Kamila001]

Thank you Dan for the suggestion, I still did not get this. I have downloaded annotation file for one of my alignments but cannot understand how will i give the position/column to be highlighted for specific sequence. Please could you explain in little detail?

[DG]

Check out the section in that link for associating an annotation track with a particular sequence. I don't know if you can automate highlighting a particular residue but you can make a seperate track that indicates a single column (perhaps with a bar graph format?) and have it linked to a particular sequence or group of sequences. Its not perfect but it may be as close as you can get in an automated fashion. You could make a histogram track for instance with a maximum score for only the column of interest and zero elsewhere, then link it to the sequence(s) of interest

Answer 2

[Ari]

If a pdf output is fine, I would do that with TeXshade: http://www.uni-kiel.de/Pharmazie/chem/Prof_Beitz/texshade.htm

Answer 3

[mg0010]

Software ResCons does this. It is a cross-OS platform software. It can highlight mismatching characters in alignment and show results in any modern browser. Available for download from https://github.com/ManavalanG/ResCons/releases