Whatever inconsistencies you see or think you see, it probably has more to do with the difference between standalone blat and gfServer/hgBlat rather than some subtle difference between different versions of blat.
gfServer version 34x2 gfServer: ELF 64-bit LSB executable, AMD x86-64, version 1 (SYSV), for GNU/Linux 2.4.0, dynamically linked (uses shared libs), for GNU/Linux 2.4.0, stripped -Galt On Mon, 11 May 2009, Jack Chen wrote: > Thanks Galt. What is the version of blat that is being used. The reason we > are asking this question is that Ismael found some inconsistencies between > the web output and the stand-alone output. > Thanks, > Jack > > On Mon, May 11, 2009 at 7:30 PM, Galt Barber > <[email protected]>wrote: > >> >> Actually this is how our gfServers are configured. >> hgBlat cgi calls these. >> >> gfServer (this is how the UCSC web-based blat servers are configured): >> >> * blat server (capable of PCR): >> gfServer start blatMachine portX -stepSize=5 -log=untrans.log >> database.2bit >> >> * translated blat server: >> gfServer start blatMachine portY -trans -mask -log=trans.log >> database.2bit >> >> >> The line you quoted is about how one run standalone >> command-line blat to approximate the behavior of hgBlat/gfServer. >> >> -Galt >> >> >> >> On Mon, 11 May 2009, Ismael Vergara wrote: >> >> Hi, >>> >>> I would like to know which blatSuite release number is the one running >>> behind >>> >>> http://genome.ucsc.edu/cgi-bin/hgBlat?command=start >>> >>> Also, I would like to confirm with you if the parameters used in the BLAT >>> web server (according to the FAQ) are: >>> >>> blat -stepSize=5 -repMatch=2253 -minScore=0 -minIdentity=0 database.2bit >>> query.fa output.psl >>> >>> Does this still applies as it is stated here? >>> >>> Thanks in advance, >>> Ismael >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >>> > > > -- > Jack Chen, Ph.D., > Associate Professor, MSFHR Scholar > Molecular Biology and Biochemistry, Simon Fraser University > SSB8111, 8888 University Drive, Burnaby, BC, Canada, V5A 1S6 > TEL: 778-782-4823; FAX: 778-782-558 > http://www.sfu.ca/mbb/People/Chen/ > http://genome.sfu.ca/orthoclusterdb/ > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
