Pairwise Sequence Alignment Of A Collection Of Proteins Scores In Matrix Format

Question

[Azam]

I am looking for the pairwise sequence alignments of a collection of proteins, and I want the alignment scores in matrix format. How can I get pairwise alignment score matrix using T-Coffee or other alignment programme?

[Lars Juhl Jensen]

I think you need to provide us with a bit more detail. Do the proteins all belong the same family so that you can make a multiple alignment, based on which you would then extract the similarity/distance between any two proteins.

[Azam]

Proteins belongs to two species of Bacteria

Answer 1

[Spitshine]

The canonical answer would be to use the phylip package protdist. The EMBOSS package might be easier to use http://emboss.bioinformatics.nl/cgi-bin/emboss/help/fprotdist

[Andreas]

I'd do the same if the sequences are aligned.

The pairwise alignment scores used by alignment programs are usually worse than the ones derived from the alignment.