Translation of protein sequence to nucleotide sequence

mathog at seqaxp.bio.caltech.edu mathog at seqaxp.bio.caltech.edu
Wed Aug 12 10:23:56 EST 1998


In article <n1af5b21mj.fsf at speed.ebi.ac.uk>, Michele Clamp <michele at speed.ebi.ac.uk> writes:
>mcbaet at MCBSGS1.IMCB.NUS.EDU.SG (Anthony Ting) writes:
>
>On a similar note and while I'm thinking of it does anyone out there
>know of something that will compare 2 protein sequences at the DNA
>level and give you the most likely DNA alignment.  I'd find this
>useful for finding possible undetected frame shift errors in multiple
>alignments.
>

The only tool that I know of which is even close is GCG's FRAMEALIGN. It
aligns a protein to DNA, allowing for frameshifts.  It is the only safe way
to go when aligning to an EST, since they have a very, very high rate of
frameshifts and other errors.  However, it assumes that the protein
sequence in the comparison is fully in the correct frame, which might not
be true if, for instance, all you had to start with is a collection of
ESTs. 

Regards,

David Mathog
mathog at seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 
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