DNA to protein in 6 frames and output in FASTA

Francis Ouellette francis at CMMT.UBC.CA
Tue Apr 20 03:32:44 EST 1999


Another www alterrnative (if you are simply looking at one sequence at
a time) is ORF-finder at:

http://www.ncbi.nlm.nih.gov/gorf/gorf.html

it links the found ORFs to BLAST for quick and easy checking as well.

cheers,

f.


--
| B.F. Francis Ouellette                     tel: (604) 875-3815  | 
| Director, Bioinformatics Core Facility     fax: (604) 875-3800  | 
| Centre for Molecular Medicine and Therapeutics, UBC, Canada     |
| francis at cmmt.ubc.ca                     http://www.cmmt.ubc.ca  |

Canadian Bioinformatics Workshop Series:
                             http://www.cmmt.ubc.ca/bioinformatics/

On Mon, 19 Apr 1999 BIOSCI-REQUEST at net.bio.net wrote:

> Date: Mon, 19 Apr 1999 22:59:24 -0700
> From: BIOSCI-REQUEST at net.bio.net, Harry Mangalam <mangalam at home.com>
> To: bio-soft at net.bio.net, phains at my-dejanews.com
> Subject: Re: DNA to protein in 6 frames and output in FASTA
> 
> 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...
> 
> 









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