Hello Amy, Updated genome assemblies change in many ways. The best place to finding information is on the Gateway page for each assembly. http://genome.ucsc.edu/ -> click on Genome Browser (left blue navigation bar) -> set clade/genome/assembly
Links on the Gateway pages to Credits will also be helpful (scroll towards bottom of Gateway page): http://genome.ucsc.edu/goldenPath/credits.html#human_credits Quote from credits page: Human Genome: Data Sources Starting with the hg19 assembly, the human genome sequence is provided by the Genome Reference Consortium (GRC), whose goal is to correct the small number of regions in the reference that are currently misrepresented, to close as many remaining gaps as possible and to produce alternative assemblies of structurally variant loci when necessary. Prior to hg19, the human genome sequence data used in the browser were generated by laboratories belonging to the Human Genome Sequencing Consortium. Periodic freezes of this data were generated by NCBI, and EST, mRNA, BACend and other types of data used for the assembly and annotation were obtained from GenBank /EMBL /DDBJ. Clone maps were created by the individual sequencing centers. Many assembly-specific details are at the Genome Reference Consortium web site: http://www.ncbi.nlm.nih.gov/projects/genome/assembly/grc/ Tools such as these in the UCSC Browser can both help map regions/data between the two assemblies to facilitate analysis, as can data from tracks in the "Mapping and Sequencing" track group. Convert - top blue navigation bar from within an assembly Batch Coordinate Conversion (liftOver) http://genome.ucsc.edu/cgi-bin/hgLiftOver Hopefully this helps, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Amy Michelle Sommer" <[email protected]> wrote: > From: "Amy Michelle Sommer" <[email protected]> > To: [email protected] > Sent: Friday, January 22, 2010 7:26:50 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] Differences between versions h18 and h19 > > To Whomever it may concern, > > I am contacting you to find out more about your genome browser > assembly from February 2009 and March 2006. I recently queried a > deletion on 14q with break points start: 52,981,656 and end: > 54,767,608 and got two different results when using the Mar. 2006 > assembly and the GRCh37 assembly. Specifically, the region I > identified on the earlier assembly was shifted thousands of bp (but > still contiguous with) the region I identified on the GRCh37 assembly > (significant change because a whole new set of genes was presented). > > Can you explain to me how this could happen? What are the differences > between the two? > > -Amy > > [email protected]<mailto:[email protected]> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
