I have E.coli protein sequences and want to compute the range of positional conservation of one amino acid (valine) across bacterial swissprot proteins. I don't really care what other amino-acids replace valine's position and therefore tools like SIFT, PROVEAN, PANTHER aren't useful as they expect 'interesting substitutions' and positions to be provided.
Eventually I used hmmer to searche for sequence homologs and generate alignments. I am at a bit of a loss how to proceed from here. Generating logos of the alignments is one option but to visually inspect them is time consuming.
What do you suggest ? Is there a tool that given a protein sequence and/or alignment can actually assess an amino-acid conservation for a large group of sequences?
Eventually I used hmmer to searche for sequence homologs and generate alignments. I am at a bit of a loss how to proceed from here. Generating logos of the alignments is one option but to visually inspect them is time consuming.
What do you suggest ? Is there a tool that given a protein sequence and/or alignment can actually assess an amino-acid conservation for a large group of sequences?
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