In article <a78dom$pup$2 at news01.cit.cornell.edu>,
dan <danwong at hongkong.com> wrote:
>>does anyone know if there's a software that would align DNA coding sequences
>based on their amino acid translation?
mrtrans - produce align cDNA sequences from aligned protein
mrtrans protein-sequence-library cDNA-sequence-library >
mrtrans is a simple program that allows you to produce
aligned cDNA sequences from aligned protein sequences. This
can be very useful for phylogeny programs, e.g. in PHYLIP -
dnadist, dnapars, dnaml, etc. In general, it is better to
use protein sequences for multiple alignments, but to use
DNA sequences for phylogeny. This can be time consuming
when there are gaps in the aligned protein sequences.
mrtrans takes a protein sequence library and a DNA sequence
library. It reads the first protein sequence and the first
DNA sequence, translates the DNA sequence in each of the
three frames, compares the protein sequence to the
translated DNA sequence to find the protein coding region,
and then writes out the DNA sequence that encoded the pro-
tein. Both libraries should be in Pearson/FASTA format. The
sequences must be in the same order in both libraries. The
protein library may include '-' characters to specify align-
ments. Each '-' character in the protein library is ignored
during the sequence comparison but replaced by '---' in the
DNA sequence output.
mrtrans finds the coding regions for contiguous sequences
only. It will not splice together different exons to pro-
duce a coding sequence.
wrp at virginia.EDU
I've just check the current location:
Gary Williams Tel: +44 1223 494522 Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.ukhttp://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK