Consensus sequence comparison

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Posted April 4, 2008 - 6:30pm by Odinten

Tags: Bioinformatics Issues

I was wondering if anybody knows of a program to compare consensus sequences to normal sequences

Thanks

Best regards

It depends what you mean by

Submitted by perlmunky on April 8, 2008 - 12:12am.

It depends what you mean by compare. Elaborate please.

TTFN

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Hi perlmunky, thanks for

Submitted by Odinten on April 9, 2008 - 5:14pm.

Hi perlmunky, thanks for your reply

I want to be able to be able to align a known consensus sequence against an uncharacterised protein sequence and if possible be able see if the residues of the uncharacterised sequence fit with in the consensus amino acid code (e.g o = S,T; l = I,L,V; . = A,C,D,E,F,G,H,I,K,L,M,N,P,Q; etc) to which it is aligned.

e.g (consensus and protein sequence taken from SMART for the TPR domain) A program which would align S75991 against the consensus sequence and identify the residues which correspond to the consensus amino acid code.

S75991 ALTLNNIGTIYYAREDYDQALNYYEQALSLSRAV
CONSENSUS/80% ..hh.thu.hh...tphppAht.hppsltht.p.
CONSENSUS/65% spshhphGthhhphsphppAlphappAlplpsp.
CONSENSUS/50% spsatslGpsatptucaccAlcsap+ALclsPss

Best regards

Does this not make sense? or

Submitted by Odinten on April 12, 2008 - 5:11pm.

Does this not make sense? or is it not possible to do?

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