Question: Single Position Highlight In Multiple Sequence Alignment
1
gravatar for Kamila001
7.1 years ago by
Kamila001120
Kamila001120 wrote:

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.

multiple • 2.5k views
ADD COMMENTlink modified 23 months ago by Biostar ♦♦ 20 • written 7.1 years ago by Kamila001120

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

ADD REPLYlink written 7.1 years ago by Neilfws48k

true … its homologous sequences i guess?

ADD REPLYlink written 7.1 years ago by Kamila001120

True… its homologous sequences i guess

ADD REPLYlink written 7.1 years ago by Kamila001120
3
gravatar for Dan Gaston
7.1 years ago by
Dan Gaston7.1k
Canada
Dan Gaston7.1k wrote:

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

ADD COMMENTlink written 7.1 years ago by Dan Gaston7.1k

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?

ADD REPLYlink written 7.1 years ago by Kamila001120

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

ADD REPLYlink written 7.1 years ago by Dan Gaston7.1k
1
gravatar for Ari
7.1 years ago by
Ari110
Ari110 wrote:

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

ADD COMMENTlink written 7.1 years ago by Ari110
0
gravatar for mg0010
2.6 years ago by
mg001010
mg001010 wrote:

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

ADD COMMENTlink written 2.6 years ago by mg001010
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1137 users visited in the last hour