How to add the amount of conservation (*);(:);(.) to an established multiple sequences alignment?
2
0
Entering edit mode
6 months ago

I would like to add the conservation data to my multiple sequences alignment (i generated it before, but it was saved in FASTA format and i don't have the conservation data; '*': Exact, ':': Conserved Substitution, '.': Semi-conserved substitution). Is there any way to do it? Thank you.

alignment msa conservation • 462 views
ADD COMMENT
1
Entering edit mode
6 months ago
Mensur Dlakic ★ 12k

This is not exactly what you are asking for, but still it may be helpful.

http://prodata.swmed.edu/al2co/al2co.php

In one of its several outputs it will print a number above each alignment column, where 9 is absolutely conserved and 0 is completely random. The program can be downloaded here for local use.

ADD COMMENT
0
Entering edit mode

I will try it, thank you for your recommendation.

ADD REPLY
0
Entering edit mode
6 months ago

For anyone who has the same question, you can use unipro UGENE to save as the multiple sequence alignment along with the conservation data (as a Clustal file format).

ADD COMMENT

Login before adding your answer.

Traffic: 1268 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6