In article <Andy.Law-1610951734030001 at pc0734.ri.bbsrc.ac.uk> Andy Law,
Andy.Law at bbsrc.ac.uk writes:
> > What I want to do is search all 6 possible orfs of specific
> > with a very short peptide sequence (6 - 10 aa in length). The
> > sequences are the complete sequences of human herpesviruses, each
> > >150,000 bp in size.
>>FINDPATTERNS ?? If I understand your requirements correctly
>Not exactly... FINDPATTERNS (GCG package) doesn't search nucleotide
translated "on the fly" in all 6 frames for a peptidic pattern...
But it doesn't actually need complex modifications of the source to
change it into
TFINDPATTERNS which does exactly that...
It doesn't do the preselection of human herpesviruses complete genomes as
SRSFASTA though ;o) ...
plewniak at igbmc.u-strasbg.fr