[Biojava-l] Help

[Schreiber, Mark]

Hi -
 
Take a look at BioJava in Anger (http://www.biojava.org/docs/bj_in_anger/) hopefully that will help you learn some of the biojava basics (if not let me know which areas are not well covered and we can update them).
 
Specifically I think you want to use the WeightMatrix classes (from the org.biojava.bio.dp) package. Take a look at http://www.biojava.org/docs/bj_in_anger/weightMatrix.htm for a simple example of how they are used.
 
Hope this helps,
 
Mark
 

	-----Original Message----- 
	From: Hailong Meng [mailto:hmeng at cise.ufl.edu] 
	Sent: Sat 26/07/2003 8:13 a.m. 
	To: biojava-l at biojava.org 
	Cc: 
	Subject: [Biojava-l] Help
	
	

	Hello,
	
	I am new to this list. I am planning to write a Java program to do
	some alignments. Basically, the Java program will read two
	files. One has a list of motif matrixes and the other has a list of
	sequences. My java program will scan the sequence file to find the
	sequence which have the high scores when they are compared with the
	motifs.
	
	I hope that I can use BioJava to save time for this program and also
	for my future project. I have read the tutorial and JavaDoc API for
	several days. But, I find that I am still confused and it is hard for
	me to find the classes I want to use. I'll very appreciate if someone
	can give me some advices about how to be familiar with BioJava.
	
	Thanks a lot!
	
	Hailong
	
	--
	
	
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