Software for ungapped local alignment with custom substitution matrix

Question

[cl10101]

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.

Answer 1

[ksi216]

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

Answer 2

[Suzanne]

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.