6-frame EST translation

walker at ncbi.nlm.nih.gov walker at ncbi.nlm.nih.gov
Fri Sep 25 08:09:32 EST 1998

[botka writes]
> Jonathan Epstein wrote on Thu, 24 Sep 1998:
>> 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.
> I believe the SEALS package has a program called wimklein that will  
> do this for you.  It's all perl, so it should work for you.
> http://www.ncbi.nlm.nih.gov/Walker/SEALS

(Hi Jonathan)

You can indeed use wimklein to do a simple 6-frame translation

  wimklein est.fa -frames= all -quiet     # -quiet keeps it from whining
                                          # about bogus codons

Most of the SEALS installation can be skipped if you just want to run a
script like wimklein.  Having a recent perl should be sufficient.  If the
script complains about a module being missing, just set -screen_width on
the command line.

In what form do you have the mass-spec data ?



Roland Walker
walker at ncbi.nlm.nih.gov
National Center for Biotechnology Information

More information about the Bio-soft mailing list

Send comments to us at biosci-help [At] net.bio.net