Hello, As you noticed, when the alignment was generated at UCSC you used BLAT and when the alignment was generated at NCBI you used BLAST. These are two completely different alignment programs. Different alignment programs and the parameter options within a single alignment program can all produce difference results. Which result is "best" depends on the experiment and is up to the scientist doing the analysis to determine.
Here is a quick explanation of the two programs (the entire BLAT FAQ may be interesting to you): http://genome.ucsc.edu/FAQ/FAQblat#blat1 Good luck with your project, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Fanlou Kong" <[email protected]> wrote: > From: "Fanlou Kong" <[email protected]> > To: [email protected] > Sent: Tuesday, December 1, 2009 11:58:37 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] a gene's position on chromosome at UCSC assembly(feb-2009) > is different from position at NCBI built > 37 > > Dear Sir or Madam, > I blat the gene NF1(human) in UCSC Genome Browser(feb-2009) and get > the > gene's begaining position ==chr17:29,446,152,but when I blast the same > gene > human NF1 in NCBI ,however the gene's begaining position > ==29,421,995,and I > know UCSC(feb-2009)and NCBI built 37 are identical and so why could > this > happen?could you help me please? > thanks. > Regards > KFL > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
