Hello Yu, While we cannot offer help with java per se, you will probably find the blat and gfClient command line utilities useful:
http://genome.ucsc.edu/FAQ/FAQblat#blat3 Note that program-driven use of the Genome Browser software is limited to a maximum of one hit every 15 seconds and Blats sequences in batches of 25 sequences at a time. You can find a script written to obey this usage limit written by one of our engineers here: http://genomewiki.ucsc.edu/index.php/Blat_Scripts Hopefully this provides a good starting point for your work. If you have further questions require genome browser usage you can contact the mailing list at [email protected]. Regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 08/11/11 17:25, Yuan Jian wrote: > thanks Vanessa. > It is appreciated if you can give more information how to call blat from > java. > Yu > > > > From: Vanessa Kirkup Swing <[email protected]> > To: Yuan Jian <[email protected]> > Cc: "[email protected]" <[email protected]> > Sent: Friday, 12 August 2011 9:01 AM > Subject: Re: [Genome] blat server > > Hi Yuan, > > Our engineer doesn't see that there is support in BioJava for calling > blat and processing the psl format. We suggest that you contact > BioJava for more information. You could run your own blat instance > locally and execute it from java. > > Here is information on downloading blat: > > http://genome.ucsc.edu/FAQ/FAQblat.html#blat3 > > Hope this helps you! If you have further questions, please contact > the mailing list: [email protected]. > > Vanessa Kirkup Swing > UCSC Genome Bioinformatics Group > > > > ---------- Forwarded message ---------- > From: Yuan Jian <[email protected]> > Date: Thu, Aug 11, 2011 at 12:48 AM > Subject: [Genome] blat server > To: "[email protected]" <[email protected]> > > > Hello dear UCSC supporters, > > is it possible to use java or biojava to call blat server remotely? > and how to do if can? > > thanks > YU > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
