program to extract the three codon positions?

Hassan Badrane hbadrane at pasteur.fr
Fri Nov 15 09:12:30 EST 1996


Keith Bradnam wrote:
> 
> Hassan Badrane  <hbadrane at pasteur.fr> wrote:
> >I 'm looking for a software (mac, dos, unix) which from an alignement of
> >sequences, gives three alignements each corresponding to the three
> >positions in the codons.
> 
> I've never seen any program offer anything like this.
> I'd imagine you'd have to write your own program/script to do it.
> 
> What you want, might be problematical if you have alignments
> of ORFs with insertions.
> 
> E.g. if you had the following three short ORFs:
> 
> ATG AAT CGG TAC TAA
> ATG ATC GGT ACT TAA
> ATG TTC CGA TCC TAA
> 
> Clustalw aligns these as:
> 
> 1               ATGAATCGGTACTAA-
> 2               ATGA-TCGGTACTTAA
> 3               ATGTTCCGATCCTAA-
>                 ***   ** * ** *
> 
> The single insertion in one sequence would mean that you
> would then have problems in extracting alignments of 1st,
> 2nd, 3rd base positions etc.
> 
> Keith B.

Thanks Keith for your detailed response. the probleme of the gaps can be
avoided by first doing alignement of proteins and then aligne
nucleotides from proteins.
but as you stated before, it seems no program do extracte different
codon positions from an alignement.

Hassan B.




More information about the Bio-soft mailing list