program to extract the three codon positions?

Keith Bradnam 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:

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.

Dept. of Genetics
University of Nottingham.
-- 
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