[Biojava-dev] Fwd: Re: [Biojava-l] locating genes in a genomic sequence

[Matthew Pocock]

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In practice, how far from a 1.3.0 release are we?

Matthew

 Note: forwarded message attached. 

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From: Karin Lagesen <karin.lagesen@labmed.uio.no>
To: "Schreiber, Mark" <mark.schreiber@agresearch.co.nz>
Cc: biojava-l@biojava.org
Subject: Re: [Biojava-l] locating genes in a genomic sequence
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Date: Wed, 8 Jan 2003 09:40:36 +0100
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On Wed, Jan 08, 2003 at 09:28:37AM +1300, Schreiber, Mark wrote:
> 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.

Thankyou for your help. However, I seem to have a different version of
biojava than you, since I cannot find that class in that package (and
not in none of the others either). The biojava I am using is version
1.22 downloaded from biojava.org. I did however discover a
KnuthMorrisPrattSearch in a biojava API at
http://rosetteer.icu.ac.kr/, however, I could not figure out how to
get at the actual class....

Am I missing something again?

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