Sequence alignment matrix

Question

[Hansen_869]

Hi there,

I'm searching for a sequence alignment tool that can provide me with a matrix like the one on the attached image. I need the 4 parameters Identity(%), Homologs (identical + conserved + weakly conserved), Unconserved and Coverage for all combinations AB, AC, CB etc. I have about 20 sequences this needs to be performed on. I have tried with ClustalW, but I only get an Identity matrix and not the other 3 parameters. If you know of any such service out there that'll provide me with this (without having to manually use pairwise alignments on all sequences) It'll be greatly appreciated!

Thanks!

Answer 1

[GenoMax]

Looks like clustalo can do this:

Make matrix of protein pairwise identities/similarities from multiple protein sequences

[Hansen_869]

Thanks for the suggestion. Never got it to work though, but ended up using MatGAT instead.

[GenoMax]

Can you include a link for MatGAT for future visitors?

Answer 2

[Hansen_869]

Sure, here you go! https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-4-29

[Mensur Dlakic]

Without any intention to knock down this particular tool, this is a 20-year old program. I doubt it will do a better job than modern implementation such as Clustal Omega. What exactly is it that you can't get clustalo to do? There are binary files to download for most common computers, and from that point on it is simply a matter of using appropriate command-line switches.

I'd be very surprised if there is a tool doing exactly what you want. Your expected output is not a matrix but rather some kind of concatenation of multiple matrices. BLASTp has an option for pairwise alignments of two sequences from which you should be able to extract the info you want. This could be doable programmatically through BioPython.