more ?s on alignments and S/NS substitutions

Jerry Learn learn at u.washington.edu
Fri Feb 6 12:05:07 EST 2004

In addition to SeqLab and MRTRANS (see article
c00fsg$5gg$1 at mercury.hgmp.mrc.ac.uk from "Steve Thompson"
<stevet at bio.fsu.edu>), I have a couple of suggestions.

I'm pretty sure there is an undocumented feature in the MacClade program
(http://macclade.org, $125) that does this. I have not used this feature
myself, but I've heard that it works.

In addition, gde (predecessor of SeqLab initially written for SunOS by Steve
Smith, but ported to Linux and MacOS X,
http://www.msu.edu/~lintone/macgde/), works very nicely for manual editing
of the nucleotide sequence to correspond to an amino acid alignment -- if
you opt for this, be sure to investigate the Sequence Grouping funtion.

An additional and unsolicited comment: when you follow this procedure, keep
in mind that while most (virtually all?) viable indel mutations happen in
triplets, not all of these events happen between codons; it might be prudent
to exclude the codons adjacent to the indel gap unless you are sure that all
three positions share positional homology.

Hope this helps.

On 2/4/04 8:34, in article bvr6vh$6ih$1 at mercury.hgmp.mrc.ac.uk, "Thomas
Isenbarger" <isen at molbio.mgh.harvard.edu> wrote:

> Hello all:
> I have a clustalw alignment of homologous nucleotide sequences from 5
> microbial genomes.  I want to quantify the synonymous/nonsynonomous
> substitutions along the length of the alignment on a codon-by-codon
> basis.
> I am interested in the nucleotide sequences here, not the amino acid
> sequences.
> 1.  can anyone suggest a method (freely available software would be nice
> too) for aligning the nucleotide sequences using the translated amino
> acid sequence as a guide?  if not, can anyone recommend an alignment
> viewer for multiple alignments that allows one to view both the
> nucleotide sequence and translation simultaneously for all sequences in
> the alignment? (so I can adjust the nucleotide alignment by hand)
> then, can anyone suggest good software for processing the alignment to
> do the substitution quantification I mentioned above?
> Thank-you,
> Tom Isenbarger
> ---

Jerry Learn

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