> 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.
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 ?
walker at ncbi.nlm.nih.gov
National Center for Biotechnology Information