DNA to protein in 6 frames and output in FASTA

Harry Mangalam mangalam at home.com
Tue Apr 20 00:59:24 EST 1999


This will do that exactly and you don't even have to download anything:

http://hornet.bio.uci.edu/~hjm/projects/tacg/tacg2.form.html

The bit that you want is " Stream out Open Reading Frames " - you can
choose the minimum size of ORF.

There is an 'oddity with this version in that it spits out the data in 1
long line, but that's easy to wrap in an editor (you can pick either
this method or the wrapped output in the current version, but I haven't
created the Web interface for it yet).

If you either like it or don't like it, let me know. 
If you want the source code or binaries, try:
ftp://mamba.bio.uci.edu/pub/tacg

Bernard Murray (bpmurray at cgl.ucsf.edu) just emailed me to say that he
had created a DJDPP version of tacg so that it would run under DOS, and
there's a win32 (CLI also) version that will also run under win9x/NT
that was ported by  Can Tran <cvtran at ucsd.edu>.  get in touch directly
for their ports.

I'm currently trying to make version 3 compile under cygwin...

-- 
Cheers,
Harry
Harry J Mangalam -- (949) 856 2847 -- mangalam at home.com


> I am looking for software (Win9X/NT or UNIX) that will translate a given DNA
> sequence (in FASTA format) in all six frames and then output this translation
> in FASTA format. Ideally, it will be able to identify ORFs and exclude
> non-ORF regions. ie. we want to translate a DNA database into a protein
> database. If anyone can help with this it would be appreciated.




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