Hi - For a 'manual' of biojava, take a look at the documentation section of the biojava wiki (www.biojava.org). Specifically the tutorial (http://biojava.org/wiki/BioJava:Tutorial) and the cookbook (http://biojava.org/wiki/BioJava:CookBook).
There is more than one way to get an ORF prediction. One way would be to do a six frame translation (http://biojava.org/wiki/BioJava:Cookbook:Translation:SixFrames) a more sophisticated way would be to make a Hidden Markov Model that distinguishes coding ORFs from non coding ORFs. You could do this using the DP package. There is no specific tutorial but you can get some hints from the Dynamic Programming part of the cookbook. One of the interesting things about BioJava is that it is much more low level than something like EMBOSS. Rather than doing lots of things it enables you to write your own programs to do things. Hope this helps. Welcome to BioJava. - Mark On Sun, Mar 23, 2008 at 2:42 PM, Kuan Yang <[EMAIL PROTECTED]> wrote: > Hi Guys, > > I am new to biojava and don't know how to do a lot of things with it. > One of them is how to get ORF prediction with it. Any help will be > appreciated. > BTW, Is there a detailed manual for it? > > Thanks > > Kuan > _______________________________________________ > Biojava-l mailing list - [email protected] > http://lists.open-bio.org/mailman/listinfo/biojava-l > _______________________________________________ Biojava-l mailing list - [email protected] http://lists.open-bio.org/mailman/listinfo/biojava-l
