BLAST/FASTA search of a specific sequence

Frederic PLEWNIAK plewniak at igbmc.u-strasbg.fr
Tue Oct 17 10:13:04 EST 1995


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
sequences 
> >  with a very short peptide sequence (6 - 10 aa in length).  The
specific 
> >  sequences are the complete sequences of human herpesviruses, each
one is 
> >  >150,000 bp in size.
> >  
>
>FINDPATTERNS ?? If I understand your requirements correctly
>
Not exactly... FINDPATTERNS (GCG package) doesn't search nucleotide
sequences
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) ...

Frederic Plewniak
plewniak at igbmc.u-strasbg.fr




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