DNA-protein alignment

[Carolyn Weiller]

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.


The public domain java program package "TransAlign" does exactly that.
Including reading Fasta file format.
TransAlign in available on
http://life.anu.edu.au/molecular/software/transalign/

==================================
Dr Georg Weiller
Head, Bioinformatics Group
Research School of Biological Sciences
Australian National University
GPO 475, Canberra, ACT 2601
AUSTRALIA
phone +61 (0)2 6249-5916
fax  +61 (0)2 6279-9709
www  http://biology/rsbsweb/profiles/georgw.shtml