Biostar Beta. Not for public use.
compare subsets of sequences in multiple alignments
0
Entering edit mode
15 months ago

Hi! I am interested in inferring whether a subset of sequences extracted from a multiple alignment has several sequence peculiarities (e.g.: a hyper-conserved base at some position). Are there any tools which take as input the alignments? Alternatively, which statistics should I use? Thanks!

ADD COMMENTlink
2
Entering edit mode
16 months ago
Bergen, Norway

Jalview can do this. You can also select a subset of rows and colums and compute a new alignment on the fly.

ADD COMMENTlink
2
Entering edit mode
2.4 years ago
Suzanne • 60
Dundee, Scotland

Jalview is a free protein and nucleic acid sequence alignment visualisation software that can compare subsets of sequences in multiple alignments. I suggest you check out the video on 'selecting residues, sequences and columns of proteins' (https://youtu.be/WUTlDJO9xxQ). This is one video in Jalview YouTube 'selecting and editing sequences' playlist (https://www.youtube.com/playlist?list=PLpU3VZmUmrT27N2Uy32qszCOoznvN-07N). The program can be launch from http://www.jalview.org/.

ADD COMMENTlink
0
Entering edit mode

Thanks for the detailed instructions.

ADD REPLYlink

Login before adding your answer.

Similar Posts
Loading Similar Posts
Powered by the version 2.1