aligning DNA sequences according to their amino acid translation

[Gary Williams]

In article <a78dom$pup$2 at news01.cit.cornell.edu>,
dan <danwong at hongkong.com> wrote:
>Hi,
>
>does anyone know if there's a software that would align DNA coding sequences
>based on their amino acid translation?

NAME
     mrtrans - produce align cDNA sequences from aligned  protein
     sequences


SYNOPSIS
     mrtrans  protein-sequence-library  cDNA-sequence-library   >
     aligned-cDNA-sequences


DESCRIPTION
     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.

AUTHOR
     Bill Pearson
     wrp at virginia.EDU


I've just check the current location:
ftp://ftp.virginia.edu/pub/fasta/other/mrtrans.shar


Regards,
Gary

Gary Williams               Tel: +44 1223 494522  Fax: +44 1223 494512
mailto:G.Williams at hgmp.mrc.ac.uk            http://www.hgmp.mrc.ac.uk/
Bioinformatics,MRC HGMP Resource Centre,Hinxton,Cambridge, CB10 1SB,UK