alignment software

Will Fischer wfischer at sunflower.bio.indiana.edu
Tue Jan 27 18:16:42 EST 1998


Junaid Gamieldien (junaid at techno.sanbi.ac.za) wrote:
: Does anyone know of software that can make a DNA multiple alignment
: from protein a aligment? DNA sequences are available (DNA versions of
: protein sequences).

My Perl script, align2aa, does just that.

See http://www.bio.indiana.edu/~wfischer/Perl_Scripts/

(Perl is FREE, and available for most common operating systems)

Summary: align2aa 

       insert gaps into a DNA sequence alignment to match a
       corresponding amino-acid alignment.

       Takes two or more input files (order unimportant) containing
       sequences, writes a new output file in fasta format with the
       named after one input file (suffix stripped) + 'aligned2aa'.
       Also writes a file of the amino-acid alignment gapped to line up
       neatly with the nucleotides (*.gapped_aas). With the -i option
       (see below) the gapped amino-acid sequences are interleaved with
       the nucleotide sequences.

       Both fasta- or GenBank-format are supported by default; if Don
       Gilbert's highly useful readseq program is installed in the
       user's path, align2aa will use it to handle most other common
       sequence formats.

       Like nt2aa, align2aa supports specifying genetic codes for
       individual sequences with a GenBank-style /transl_table=#
       qualifier in either amino- or nucleic-acid sequence (fasta and
       GenBank formats only).  --
____________________________________________________________
Will Fischer

Biology Department             		wfischer at indiana.edu
Jordan Hall                   		http://www.bio.indiana.edu/~wfischer
Indiana University            		Lab:    812-855-2549
Bloomington, Indiana 47405 USA		FAX:    812-855-6705




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