[Biojava-l] locating genes in a genomic sequence

[Schreiber, Mark]

Hi -

If you already have the SimpleGene features constructed these will
contain a Location object. However, I think you are saying how can I
find a subsequence in my Genomic sequence and locate the gene that way?

To rapidly find exact matches you can use the biojava
KnuthMorrisPrattSearch object from the org.biojava.bio.search package.
It contains a main method that demonstrates it's use. This is a very
efficient algorithm for finding exact matches.

Note: if the genome is larger than 64kb you will not be able to dump it
as a String as that is the maximum String length. You could dump it as a
char[].

- Mark


> -----Original Message-----
> From: Karin Lagesen [mailto:karin.lagesen@labmed.uio.no] 
> Sent: Tuesday, 7 January 2003 10:53 p.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] locating genes in a genomic sequence
> 
> 
> 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 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org 
> http://biojava.org/mailman/listinfo/biojava-l
> 
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