6-frame EST translation

Tim Cutts timc at chiark.greenend.org.uk
Fri Sep 25 06:19:32 EST 1998


In article <360AB021.F9E940B0 at nih.gov>,
Jonathan Epstein  <Jonathan_Epstein at nih.gov> wrote:
>Does anyone have a working program that can compare
>mass-spec ion sets obtained from an LCQ instrument against the dbEST
>database?
>
>This seems to require a 6-frame translation of dbEST, preferably in
>FASTA format.  I realize that many of the translated products will be
>bogus.
>
>Does anyone have software to perform this translation?  The preferred
>target platform is a DEC alpha running Unix, but Wintel 95/NT and SGI
>Irix are also possible candidates.

I wrote a (quite fast) program in C to do precisely this.  It takes a
nucleic acid database in fasta format as input, and produces six fasta
format protein databases as output.  It's part of my tpatterns
package (a sort of findpatterns that translates nucleic acid databases
on the fly)

Obviously, you need to get dbEST into fasta format first, but you may
already have that, especially if you use BLAST locally.

I've never officially released tpatterns, but you can download it from:

http://www.bio.cam.ac.uk/~tjrc1/software/tpatterns/tpatterns-1.0.tar.gz

You just want the txfasta program, rather than the whole package, so
after unpacking it, modify the Makefile (if necessary) and do:

make txfasta

Tim.

PS.  Users of multi-CPU machines may be interested in a preliminary MPI
version of  tpatterns.  The MPI version has been run successfully on
both a 4 CPU Origin 200, and also on a Hitachi SR2201 massively
parallel supercomputer.
Contact me if you are interested.






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