Software for ungapped local alignment with custom substitution matrix
2
0
Entering edit mode
5.6 years ago
cl10101 ▴ 80

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.

local alignment blast substitution matrix • 1.7k views
ADD COMMENT
1
Entering edit mode
ADD COMMENT
0
Entering edit mode
5.6 years ago
Suzanne ▴ 80

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 COMMENT

Login before adding your answer.

Traffic: 3175 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