? about DNA alignment

Peter Stockwell peter at sanger.otago.ac.nz
Thu Jun 24 16:00:44 EST 1993

Elliot Lefkowitz (lefkowitz at orion.cmc.uab.edu) wrote:
> 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
> the
> >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

> **************************************************************
> *  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               *
> **************************************************************

It is obviously time to mention again my HOMED Homologous sequence
editor which has the capability to display and edit nucleic acid
sequences as their peptide translations.  Gapping/editing of the
underlying nucleic acid sequence is performed appropriately as the
peptide sequences are edited.  The program also has interfaces to AMPS,
PHYLIP, CLUSTAL(V) and GCG formats.

HOMED is presently implemented on VAX/VMS and DEC/Ultrix platforms and
is written in Pascal.  It is available by anonymous ftp from OTAGO.AC.NZ
( in the directory OU:[ANONYMOUS.PUB.BIOC06].  Files are:

homed.svs              VMS backup
homed.tarz             Compressed tar
homed_src.lzc          lzcmp compressed VMS BACKUP, sources only
homed_src.svs          VMS backup, sources only.

Any problems/queries, please contact

Peter A. Stockwell
peter at sanger.otago.ac.nz

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