Hello, A double check confirms that both browsers are presenting the same version of genomic, the same version of the RefSeqs, and we can confirm your coordinates. The differences are small and appear to be due to the different alignment tool(s) used.
The UCSC Genome browser aligns RefSeq sequences using BLAT. The hapmap.org alignments are most likely aligned using BLAST (no documentation found at their web site, but you could email them to ask). If this does not address your concerns, please let us know, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "BRJoyce" <[email protected]> wrote: > From: "BRJoyce" <[email protected]> > To: [email protected] > Sent: Wednesday, September 23, 2009 1:04:17 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] different gene locations > > I was looking at various genes on UCSC's gene browser and hapmap.org's > > gene browser and they don't seem to match up. For example the > locations > of the nucleotides do not match up on various genes using the two > sites' > browsers. > > NM_030881 yields these different positions and lengths from the > different sites. > 37,209,389 to 37,214,481 //ucsc > 37,209,391 to 37,214,912 //hapmap.org > > NM_024324 > 48,698,287 to 48,707,190 //ucsc > 48,698,348 to 48,707,178 //hapmap.org > > NM_007310 > 18,330,070 to 18,337,496//ucsc > 18,330,070 to 18,336,528 //hapmap > > If I am not mistaken, ucsc and hapmap both are working off of build > 36.1 > from www.ncbi.nih.gov Any guidance would be much appreciated.--Ben > > ( The browsers are located at > http://genome.ucsc.edu/cgi-bin/hgGateway?org=Human&db=hg18&hgsid=143903444 > http://hapmap.ncbi.nlm.nih.gov/cgi-perl/gbrowse/hapmap3r2_B36/ > ) > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
