Translation program for PCs

Keith James k.james at bangor.ac.uk
Tue Aug 5 11:55:38 EST 1997


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
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