Hi Jia, Alignments between the two genomes are constructed with lastz, formally known at blastz. Please see http://genome.cshlp.org/content/13/1/103.abstract for more information. Also, please see this previously answered question which may be useful for you: https://lists.soe.ucsc.edu/pipermail/genome/2011-May/025889.html
--- Luvina Guruvadoo UCSC Genome Bioinformatics Group Zeng, Jia wrote: > Hi, Luvina: > > Thank you for your quick response. It turns out this tool is very helpful to > my specific question. > > I just have one more question. When the liftOver tool perform the coordinates > conversion from human genome to the chimpanzee genome, dose it based upon the > BLAT alignment, or any other resource? Thanks. > > Jia > > ----- Original Message ----- > From: "Luvina Guruvadoo" <[email protected]> > To: "Jia Zeng" <[email protected]> > Cc: "genome" <[email protected]>, [email protected], "Soojin Yi" > <[email protected]> > Sent: Friday, May 6, 2011 2:43:50 PM > Subject: Re: [Genome] Question about human and chimpanzee comparative analysis > > Hi Jia, > > The Batch Coordinate Conversion (liftOver) utility is a useful tool for > converting coordinates between assemblies. From the main page, click on > 'Utilities' located on the left-side menu, then click on 'Batch > Coordinate Conversion (liftOver)'. Here, you can select your original > genome/assembly (human/hg18) and new genome/assembly (chimpanzee), and > upload your BED file. Once you have submitted your data, scroll down and > click on 'View Conversions'. Your results will be displayed in BED format. > For general information on how to use the liftOver utility, see: > http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Convert. > > Please feel free to search the Genome mailing list archives by visiting > our home page and clicking on "Contact Us" > (http://genome.ucsc.edu/contacts.html), or email us again at > [email protected] if you have any further questions. > > --- > Luvina Guruvadoo > UCSC Genome Bioinformatics Group > > > Zeng, Jia wrote: > >> To whom it may concern: >> >> I would like to use UCSC genome browser to do some comparative analysis >> between human and chimpanzee. Right now I have the genome coordinates for >> the region of interest in human (hg18), and I would like to look for the >> orthologous site in the chimpanzee genome. >> >> I have the coordinates in human as BED format, here is the part of the file: >> >> chr11 66346610 66346721 3 200 + >> chr14 90693735 90693787 4 200 + >> chr3 197937922 197938039 5 200 + >> chr1 143729237 143729356 6 200 - >> >> I wonder if I can directly use this file as an input, and utilize some tool >> in UCSC genome browser to directly get the coordinates of orthologous site >> in the chimpanzee. It would be nice if the output file has the same format >> as my input. >> >> Thank you so much and I am looking forward to your reply. >> >> Best, >> >> Jia Zeng >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
