[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 se

[Biojava-l] Newbie Question 2: Searching Sequences for regular expressions

Is there any way to search a sequence for a regular expression? Andy Hammer University of Utah Human Genetics ___ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l

FW: [Biojava-l] Newbie Question 2: Searching Sequences for regular expressions

Sorry meant to forward this to the list... -Original Message- From: Schreiber, Mark Sent: Thursday, 24 October 2002 11:09 a.m. To: 'andy hammer' Subject: RE: [Biojava-l] Newbie Question 2: Searching Sequences for regular expressions To clarify... There is not yet any formal RE parser t

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

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.bioj

Re: FW: [Biojava-l] Newbie Question 2: Searching Sequences forregular expressions

Hello Mark, Andy Keith added a CharSequence wrapper around SymbolList to the src-1.4 repository, so with the java 1.4 version of biojava you can do something like SymbolList s1 = { AATGG }; SymbolList s2 = { some long seq }; Pattern p = Pattern.compile( MotifTools.createRegex(s1) ); SymbolL

RE: [Biojava-l] "packed" SymbolLists?

Hi - There is a PackedSymbolList and a PackedDNASymbolList in org.biojava.bio.symbol. Can't say I've used them but I think they operate pretty much the same as normal SymbolLists. - Mark > -Original Message- > From: Dave Barkan [mailto:dbarkan@;snowball.pcbi.upenn.edu] > Sent: Thursday

[Biojava-l] "packed" SymbolLists?

Hey all, I saw in the tutorial on the Biojava home page that it is possible to implement a "packed" symbolList that only uses 2-4 bits per nucleotide. Is there a class available that implements this yet? (If not, what is the reasoning behind this and would it be something I could easily set up an

[Biojava-l] JDK1.4 and BJ1.3

Hi - The 1.4 JDK has been around for quite a while know and is available for all the usual OS and IDE suspects. Might it be time to officially merge all of the 1.4 stuff into Biojava? Possibly making another release, biojava1.3? - Mark Mark Schreiber PhD Bioinformatics AgResearch Invermay PO Bo