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: [EMAIL PROTECTED] > 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 - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > ======================================================================= Attention: The information contained in this message and/or attachments from AgResearch Limited is intended only for the persons or entities to which it is addressed and may contain confidential and/or privileged material. Any review, retransmission, dissemination or other use of, or taking of any action in reliance upon, this information by persons or entities other than the intended recipients is prohibited by AgResearch Limited. If you have received this message in error, please notify the sender immediately. ======================================================================= _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
