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