FW: [Biojava-l] Newbie Question 1: Searching Sequences

[Schreiber, Mark]

Sorry meant to forward this to the list

-----Original Message-----
From: Schreiber, Mark 
Sent: Thursday, 24 October 2002 11:07 a.m.
To: 'andy hammer'
Subject: RE: [Biojava-l] Newbie Question 1: Searching Sequences


Hi -

To find an exact match you can use the KnuthMorrisPrattSearch from
org.biojava.bio.search package. This uses the very efficient KMP
algorithm. Probably a similar one is used by the String class.

For non-exact matches you'll probably need to use the MarkovModel
classes or the WeightMatrix class from the org.biojava.bio.dp package.
This is roughly equivalent to regular expression parsing.

- Mark


> -----Original Message-----
> From: andy hammer [mailto:ahammer@genetics.utah.edu]
> Sent: Thursday, 24 October 2002 10:57 a.m.
> To: biojava-l@biojava.org
> Subject: [Biojava-l] Newbie Question 1: Searching Sequences
> 
> 
> In the file bootcamp_blast.tar.gz I found MotifFinder.java. It 
> searches sequences for a motiff Symbol by Symbol. If I am searching 
> 4MB file, that could take awhile. By contrast, I can search a string 
> very quickly with the
> indexOf("motiff") function. My question: Is there a better
> way to search a sequence for a motiff?
> 
> Andy Hammer
> University of Utah
> Human Genetics
> 
> _______________________________________________
> Biojava-l mailing list  -  Biojava-l@biojava.org
> http://biojava.org/mailman/listinfo/biojava-l
> 
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