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 [EMAIL PROTECTED] _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
