How i can determine to consensus sequence and conservation score " percent of conservation" for some protein? i have some genes and i want to determine these. i know in CLC and using create alignment can do it but i want another tools for this work. Thanks
1 answer
I wrote a pretty basic script which is just a wrapper to BioPython's dumb consensus method.
https://github.com/jrjhealey/bioinfo-tools/blob/master/Consensus.py
I'd look at maybe using hmmer (hmmemit) though if you want very sensitive consensus, though I think it tends to work better if there are more sequences in the mutliple alignment (but then again that's true for most MSAs).
I see the CLUSTAL Omega, it can align the sequence the amino acids of the proteins, i should get consensus sequence by common amino acids between 3 sequence? (if 2 amino acid is common alignment, it can be in consensus sequence)? and how i can calculate conservation score?
I just told you, Clustal outputs that information when you do the alignment itself.
You should really use more than 3 sequences if you want a decent consensus though, but yes, I suppose you could use 2 out of 3.
The problem you’ll have is what if all 3 sequences have different amino acids? This is why you should consider using a hmm for this.
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If these are known proteins then you could take a look at homologene database at NCBI. That should give you pre-computed alignments of homologous sequences.
A blast search followed by extaction of the related sequences and a multiple sequence alignment (using Clustal omega, MAFTT, t-coffee, muscle) would get you the alignments/consensus.