[Bio-software] Re: Exonerate

darked via bio-soft%40net.bio.net (by darek.kedra from gmail.com)
Wed Mar 21 13:57:19 EST 2007


Since man page for Exonerate does not list an option of changing codon


you may try to ask Guy St.C. Slater.  <guy AT ebi.ac.uk> who wrote it,
if there is a patch for it.
If not, wise2 http://www.ebi.ac.uk/Wise2/doc_wise2.html
has a -codon switch:

[codon.table] Codon file. The default is for the universal code, but
you can supply your own

Hope it helps,

Darek Kedra

On Mar 20, 3:09 pm, "Natacha" <natab... from gmail.com> wrote:
> Hi all,
> I try to use Exonerate,http://www.ebi.ac.uk/~guy/exonerate/, is a
> generic tool for pairwise sequence comparison. I want particularly use
> the model protein2genome with an aim to define the position of
> intron , this model will allow introns in the alignment, but also
> allow frameshifts, and exon phase changes when a codon is split by an
> intron.
> But I use a genome who have a genetic code 4, and i don't find the
> option for change the genetic code in exonerate, but I think that must
> possible. I have read the help and the manual but I haven't see this
> option.
> Somebody could help me ?
> Thanks
> Natacha

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