[Biojava-l] locating genes in a genomic sequence

[Karin Lagesen]

Hi!

I am trying to build a small program for finding intergenic areas.
This I am planning to do by locating all mRNA's in a genome and
outputting all the areas inbetween. Biojava seems to be able to help
with most of my tasks. However, I have a few questions. From what I
have understood I can have the genomic sequence as a SimpleSequence
with all of the genes as SimpleGene's attached via a FeatureHolder to
the genomic sequence. However, I have not figured out a smart way of
finding the location of each of the genes in the genomic sequence.
Since genomic sequences can be large, I hoped to avoid having to dump
the sequence in a string and use indexOf(gene sequence) to find the
position. Is there something I am missing here, or have I just
misunderstood all of this?

Thankyou in advance for your help. 

Karin
-- 
Karin Lagesen, PhD student
karin.lagesen@labmed.uio.no