Hello, BLAT was designed to run against genomic sequence. Here is a link to the Help page for this question:
http://genome.ucsc.edu/FAQ/FAQblat.html#blat1 >From a user's perspective you will notice: 1) small vs. large gaps (= intron) are scored differently 2) evalue/zscore probability is not the main statistics 3) simple statistics such as mismatch, deletion, insertion events are added up 4) the hit blocks (= exons) are output as an ordered unduplicated string 5) it is faster There are many parameter changes to adjust sensitivity. This can speed up or slow down the time it takes to run a query. Reading the BLAT documentation and testing some of these out on your own test sets would be the best way to understand the effects the options. As for query and target datasets, using the UCSC web blat, we only have genomic loaded as a target. On your own server, any dataset can be the target. You might find it useful to tune parameters for this type of case to get the best (most complete) alignment. Jen ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Mera Vigyan" <[email protected]> wrote: > From: "Mera Vigyan" <[email protected]> > To: [email protected] > Sent: Monday, September 7, 2009 12:55:38 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] why BLAT is better > > greetings, > > What is the particular reason for BLAT being better than BLAST for > doing genomic alignments ? > > thanks > Mera > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
