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:[EMAIL PROTECTED]
Sent: Sat 26/07/2003 8:13 a.m.
To: [EMAIL PROTECTED]
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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