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
>
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