Hello, Have you examined the Conservation track? This would be the first choice to answer your type of question. Use the Table browser and hg18 to extract regions based on human coordinates using web tools. Link to complete files in Downloads for ftp (see the hg18 track description for an explanation of the contents): http://hgdownload.cse.ucsc.edu/downloads.html#human scroll to Mar. 2006 (hg18), files under "Conservation" header, to obtain paths
The alternative for a direct mapping of coordinates between species is to use the liftOver program. It utilizes the chain track data (as does the net track) but is a configurable filter. The best advice is read the usage, try a few parameter sets, and evaluate. As you probably know, the syntenic relationship is not 1-1 for all cases. For some advice about how scientists here at UCSC filter for conservation, an excellent resource would be back in the Conservation track's Methodology section. Link to liftOver web tool: http://genome.ucsc.edu/cgi-bin/hgLiftOver Link to liftOver unix tool binary: http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads http://hgdownload.cse.ucsc.edu/admin/exe/ For the most recent version human->mouse, the file ftp path would be: goldenPath/hg18/liftOver/hg18ToMm9.over.chain.gz Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group ----- Original Message ----- From: jchl tu <[email protected]> To: [email protected] Sent: Tue, 14 Jul 2009 02:53:08 -0700 (PDT) Subject: [Genome] question about human-mouse genome alignment HI everyone: for I have a list of regions in the human genome and want to study if those regions have conservational counterparts in the mouse genome or not, I download "mouse net" file from Table Browser and in this file I found there may be two or even more "top" alignment region spanning the same regions in the mouse genome.as a result sometimes a same region in the human genome will have a perfect conservational region according to one "top" alignment region and may have many gaps according to another. my question is which I should trust? and if there exist a better way to study my problem please tell me (for I want to see detailed information about alignment say regionA in the human genome may have a conservational region in the mouse genome but many gaps on it, I want to see the exact coordinate of the gap and match regions). _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
