Question: Software for ungapped local alignment with custom substitution matrix
0
gravatar for cl10101
4.2 years ago by
cl1010180
cl1010180 wrote:

I'm looking for sequence alignment software used in pairwise sequence alignment , which can be used for ungapped local protein alignment with custom substitution matrix.

I found out that in NCBI blastp there is -ungapped parameter but when it comes to -matrix parameter only BLOSUM80, BLOSUM62, BLOSUM50, BLOSUM45, PAM250, BLOSUM90, PAM30, PAM70 and IDENTITY are supported and it is not possible to use custom matrices stored in text file.

I would be grateful for pointing out similar software with such a functionality.

ADD COMMENTlink modified 4.2 years ago by Suzanne70 • written 4.2 years ago by cl1010180
1
gravatar for ksi216
4.2 years ago by
ksi21670
ksi21670 wrote:

http://www.ebi.ac.uk/Tools/psa/

ADD COMMENTlink written 4.2 years ago by ksi21670
0
gravatar for Suzanne
4.2 years ago by
Suzanne70
Dundee, Scotland
Suzanne70 wrote:

Jalview is a free multiple sequence alignment software that has a powerful interactive editor that will ungapped local alignments. It runs on PCs and MACs and can be downloaded from www.jalview.org.uk. There is a Jalview YouTube video explaining how to edit gaps in proteins, RNA and DNA alignments that is in playlist on Selecting and Editing Sequences.

ADD COMMENTlink written 4.2 years ago by Suzanne70
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: 1794 users visited in the last hour