Dear Marcus,
There are two programs that I know of capable of doing this, both take
multiple sequences in the same FASTA format file and translate the ORFs
with the result being FASTA format protein sequences in a single file. The
first is FLIP, I can't remember where I found it now, but I still have it
and can send it to you if you need it. The only shortcoming is that it only
takes A, T, C, G or N, it won't accept X, R etc..
The second is TACG, an earlier version (2.38) can be accessed at
http://24.1.175.29/tacg/ This version only takes one sequence at a time.
The author has a beta test of version 3 that takes multiple sequences in
the one file (FASTA format) that you can run locally. We have had trouble
setting this up, probably more due to my lack of UNIX knowledge than
anything else. I'm pretty sure this program can cope with all the usual
IUPAC DNA degeneracies. You can get in touch with the author (Harry
Mangalam <mangalam@home.com>) to get a hold of the latest beta version. He
is very helpful and the program should suit your needs if you can get it
working on your machine.
If you need any more information, you can get back to me directly.
Regards,
Peter.
At 15:46 05/22/2000 +0200, Marcus Macht wrote:
>Dear colleagues,
>
>I would like to create a local database of protein sequences for peptide
>finger printing of an organism of which most of its sequence information is
>only available on DNA level. Since I assume that there must be a script or
>program which reads the DNA, translates it in all six ORF's and writes it
>into a FASTA compatible file already out there, I'd like to ask if you are
>aware of such a program. It should make the translation automatically
>without supervision because I've got around 200 MByte sequence data...
>Any hints will be greatly appreciated.
I'm afraid I don't have a clever saying to put here.
Peter Hains (PhD) Ph. +61 2 9850 6216
Australian Proteome Analysis Facility Fax. +61 2 9850 6200
Level 4 Building F7B E-mail. phains@proteome.org.au
Macquarie University, Sydney 2109 Web. www.proteome.org.au
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