Hello, Here is a link to an FAQ covering this question:
http://genome.ucsc.edu/FAQ/FAQblat And to double check - the primers, genome, etc. all are all the same version for both tests? BLAT and BLAST use difference algorithms to find hits. Exactly what is causing the difference may be hard to track down. But, in general some of the differences that may impact alignment locations are contained in the link above. It may also be helpful to view the regions of the matches (both BLAST and BLAT) and open up a few other tracks to see what is going on in those regions (are there repeats, genes, intron gaps?). Looking at the match locations in the context of other annotation will probably point out why the programs are producing different output. BLAST is a great tool, but there are things to watch out for when aligning to genomic sequence. BLAT is also a great tool and is the recommended tool for this particular purpose (exact matches vs genomic sequence with specificity). We hope this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- [email protected] wrote: > From: [email protected] > To: [email protected] > Sent: Friday, November 27, 2009 4:02:25 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Differences between Blast and Blat > > Dear Srs. > I am making Blat and Blast search with oligonucleotides (25 to 30 pb) > against human genome and I have differences in the results. Some > oligonucleotides match in a different region to the used for primers > design one, when I search with Blat (It does not occur with Blast). > Do > you know why could it happen? > Thank you very much. > Dr. Lucas Daurelio. > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
