[Bioperl-l] finding position of every instance of a pattern in a sequence

[Andrew Stewart]

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?


Thanks,
-Andrew Stewart