program to extract the three codon positions?
pdxkrb at evol.nott.ac.uk
Thu Nov 14 16:41:02 EST 1996
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:
*** ** * ** *
The single insertion in one sequence would mean that you
would then have problems in extracting alignments of 1st,
2nd, 3rd base positions etc.
Dept. of Genetics
University of Nottingham.
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