In the last weeks, we had many discussions on BLAST which shows that BLAST is of much interest. To my knowledge, there is no class in Biojava for invoking Blast searches yet.
Therefore I would like to discuss the new BLAST API with you. It is a Java wrapper for local NCBI and local WU-blast and for Web BLAST at http://www.ebi.ac.uk . Please have a look at the API and tell me your opinion. Have I missed something, are the method names OK ? http://www.charite.de/bioinf/strap/Scripting.html#SequenceBlaster http://www.charite.de/bioinf/strap/biojavaInAnger_SequenceBlaster.html Please send your suggestions. Here a short description: Implementations of SequenceBlaster produce XML output which can be parsed with org.biojava.bio.program.sax.BlastLikeSAXParser. There is also a simple non-Biojava DOM based parser which is currently used only to make a human readable output. The Wrapper provides a cache to avoid that one and the same BLAST is run twice. If this is, however intended, the BLAST result must be removed from the cache before invoking compute(). The implementations of NCBI and WU-blast evaluate the shell variables BLASTDB and WUBLASTDB, respectively which point to directories were the databases are located. This works even for Java1.4 where the method getenv() is corrupted. The Java wrapper can thus determine, what databases are available. The API is thread save. You can perform the computation outside the event dispatching thread. Christoph _______________________________________________ Biojava-l mailing list - Biojava-l@biojava.org http://biojava.org/mailman/listinfo/biojava-l
