[Biojava-l] locating genes in a genomic sequence

[Kalle Näslund]

Karin Lagesen wrote:

>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
>

It seems the class you cant find, KnuthMorrisPrattSearch isnt included 
in the last
official release of Biojava. But its available in the CVS source tree.
So you will have to retrieve the biojava source from CVS, and compile 
biojava.
Instructions on how to retrieve the source code from cvs can be found at 
http://cvs.biojava.org/

In order to build biojava from source you will need to have Ant 
installed ( available
from http://jakarta.apache.org/ant/index.html ). And you build it by 
just going to the
top directory of the biojava source tree, and then run ant ( run "ant 
javadocs" to build
the javadoc documentation aswell )

Kalle