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:[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 > > -- > > > _______________________________________________ > Biojava-l mailing list - [EMAIL PROTECTED] > http://biojava.org/mailman/listinfo/biojava-l > > > > ======================================================================= > Attention: The information contained in this message and/or attachments > from AgResearch Limited is intended only for the persons or entities > to which it is addressed and may contain confidential and/or privileged > material. Any review, retransmission, dissemination or other use of, or > taking of any action in reliance upon, this information by persons or > entities other than the intended recipients is prohibited by AgResearch > Limited. If you have received this message in error, please notify the > sender immediately. > ======================================================================= > _______________________________________________ Biojava-l mailing list - [EMAIL PROTECTED] http://biojava.org/mailman/listinfo/biojava-l
