[Bioperl-l] finding position of every instance of a pattern in a
astew at wam.umd.edu
Fri Sep 2 16:06:14 EDT 2005
I have problem I am trying to solve. I know I can no doubt rig up some
regular perl code to solve it, but I'm wondering if there is some
BioPerl module that might make the task much simpler.
I have a single sequence composed of a concatenation of several contigs,
with special 'contig boundary tags' marking the transition between every
of neighboring contigs.
I wrote a script that reads in the sequence, as well as glimmer output
from the sequence in order to create a series of features (for output
into a genbank file). Because any of these features spanning across
these contig boundaries probably isn't real, I also want to create a
miscellaneous feature whereever there is a 'contig boundary tag'.
Basically what I need is a function that will search the entire sequence
for my tag sequence, and return a list of the locations for every
instance of it found in the sequence.
Can anyone direct me to a module that handles this sort of thing, or do
I need to rig it up outside of bioperl?
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