[Biojava-l] Help

[Hailong Meng]

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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