DNA-protein alignment

Will Fischer wfischer at BIO.INDIANA.EDU
Wed Oct 20 13:03:28 CDT 1999

John Trueman <trueman at RSBS.ANU.EDU.AU> wanted to align DNA coding sequences
to an alignment of their encoded proteins:

    ...  To save me re-inventing the wheel does anyone have or know of a
    utility which will

    1.  input a protein alignment in one of the commonly-used formats
        (eg, Nexus, Fasta, Clustal),
    2.  input the corresponding DNA sequences, along possibly with
        leading and trailing non-coding regions and introns,
    3.  align the second to the first.

I have a perl script to do this (although it will not cope with introns).
ALIGN2AA will read fasta and other formats, and insert appropriate gaps
in the nucleotide sequences to match the amino-acid alignment.


Will Fischer

Biology Department                      wfischer at indiana.edu
Indiana University                      Lab:    812-855-2549
Jordan Hall 142                         FAX:    812-855-6705
1001 E. Third Street
Bloomington, IN  47405-3700 USA

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