[Biojava-l] Help

[Hailong Meng]

Hi, Mark,

Thank you very much for your suggestions! I am so excited when I find
BioJava. It is a wonderful place. Maybe I am new here, it is a little
bit hard for me to find the classes I want to use. Hopefully, it will
get better when I stay here a little longer.

I have one more question. I plan to search a list of motifs against a
list of sequences. I got motifs from MEME and put all the motif
matrixes to a file. I guess I need to put all these motif matrixes to
a array of WeightMatrix. How can I do that?

Thanks.

Hailong

-- 


On Sun, 27 Jul 2003, Schreiber, Mark wrote:

> 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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