Translation program for PCs

francis at NCBI.NLM.NIH.GOV francis at NCBI.NLM.NIH.GOV
Tue Aug 5 14:12:42 EST 1997

There is also "ORF finder" on the WWW (ie all platforms that run
a browser) at NCBI:


(you can also get there from our home page: http://www.ncbi.nlm.nih.gov/)

It can call any sequence in GenBank, or allow you to copy/paste your
own.  It can use all the different genetic codes we support (presently
13 different ones) and presents a clickable output (6 frames) where you
can send the selected ORF to our blast server. You can save the ORF you 
want to a FASTA file format, or GenBank format.

This perl of a utility was written by Tatiana Tatusov at NCBI. 



| B.F. Francis Ouellette  
| GenBank Coordinator
| francis at ncbi.nlm.nih.gov   

> From k.james at bangor.ac.uk Tue Aug  5 13:34:10 1997
> To: bio-soft at net.bio.net
> From: Keith James <k.james at bangor.ac.uk>
> Subject: Re: Translation program for PCs
> Date: 05 Aug 1997 17:55:38 +0100
> NNTP-Posting-Host: pwilliams.bangor.ac.uk
> X-Newsreader: Gnus v5.3/Emacs 19.34
> jclewley at hgmp.mrc.ac.uk (Dr. J.P. Clewley) writes:
> > 
> > 
> > Can anyone recommend a public domain program for PCs that will take
> > a sequence and translate it in all 6 reading frames, so that the 
> > coding strand can be identified and a file of the translated amino
> > acid sequence made.
> It won't do both strands at once, but ORF by Jean-Michel Claverie will
> get all ORFs from a sequence (it's a simple matter to rev-comp a
> sequence with text editor macro or file utility).
> You can define limits for the length of ORFs in nucleotides and it will
> print a nice summary table and a Pearson/Fasta output of translations
> sorted by size and annotated with their position in the original DNA
> sequence.
> There is C source available at ftp://ncbi.nlm.nih.gov/pub/jmc/orf/orf.c
> It compiles on Linux with a couple of errors, but seems to work. It
> may compile with a DOS/Windows version of gcc, but I haven't tried it.
> -- 
> Keith James Ph.D. - k.james at bangor.ac.uk  PGP 2.6.2i  Key ID 469A9FA1
> Biodegradation Group                         *Encrypt and Survive*  
> School of Biological Sciences    Guvf znl znxr ab frafr vs bar bs gur
> University of Wales, Bangor, UK  vasvavgr ahzore bs zbaxrlf vf bssyvar

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