? about DNA alignment

Elliot Lefkowitz lefkowitz at orion.cmc.uab.edu
Wed Jun 23 19:43:21 EST 1993

In article <ahouse-230693133550 at> Jeremy John
Ahouse, ahouse at hydra.rose.brandeis.edu writes:
>    I have done a series of multiple alignments.  The
alignments were done
>with inferred amino acid sequences.  Now that I am happy with
>alignments I want to go back to the mRNA sequence (which I
have) for some
>of the clustering and parsimony analysis.  I want to enforce
the alignments
>(gaps, etc...) from the aa's on the nucleotide alignment.
>    I know I can do this by hand, but are there any tools that
help with
>this, that you all know about?

I have been interested in exactly such a tool for some time
now. Unfortunately, I know of no program which will directly
align and gap a nucleotide sequence to a previously aligned
protein sequence. Doing this by hand especially with many
sequences is certainly tedious. The best way I know of
currently to at least semi-automate the procedure is to first
back-translate the protein sequences using the most ambigous
codon choices. Then align the nucleotide sequence to this
back-translated sequence using a program such as gap. It may
help to replace the gap characters in the back-translated
sequence with some alternate character. That way, if additional
gaps are inserted, or if the alignment is not perfect, you can
easily identify the problem areas and edit them out.

If anyone has a more direct means of doing this, I would
certainly be interested as well.


*  Elliot Lefkowitz, Ph.D.     |  University of Alabama      *
*  Lefkowitz at Orion.cmc.uab.edu |  Department of Microbiology *
*  Lefkowitz at Uabcmc.Bitnet     |  Birmingham, AL  35294      *
*                              |  205-934-1946               *

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