Ah, nevermind, found this which I believe should answer all my questions. http://genomewiki.ucsc.edu/index.php/Chains_Nets
Thanks! Bryan On Wed, Mar 17, 2010 at 11:34 PM, Bryan White <[email protected]> wrote: > Hi Vanessa, > > Thanks for the response. I have spent some time familiarizing myself with > the database. Now I'm wondering about the "ali" field in the net tables (ie. > netPanTro2). > > Is it the number of bases aligned in an alignment? So, say an "ali" is 1000 > bases long, does that mean that alignment is 1000 bases long, or does it > mean there are 1000 identical bases in that alignment, but the whole > alignment may actually be 1200 bases long. > > Thanks, > Bryan > > > On Tue, Mar 16, 2010 at 4:21 PM, Vanessa Kirkup Swing < > [email protected]> wrote: > >> Hi Bryan, >> >> The best way to view the vertebrate nets/chains is to view them in the >> human genome browser: http://genome.ucsc.edu/cgi-bin/hgGateway >> >> Here is a link to the document to help you get started: >> http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#GetStarted >> >> Once you have selected the human browser and clicked submit from the >> gateway page it will take you to that specific browser. There is a >> "Vertebrate Chain/Net" track listed under the "Comparative Genomics" section >> below the browser image. Click on the "Vertebrate Chain/Net" link to find >> out more information on this track and to set up which subtracks you would >> like to view. >> >> Please don't hesitate to contact us if you have further questions. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> ----- Original Message ----- >> From: "Bryan White" <[email protected]> >> To: [email protected] >> Sent: Tuesday, March 16, 2010 2:08:15 PM GMT -08:00 US/Canada Pacific >> Subject: [Genome] .net and .chain files >> >> Hello, >> >> I am currently trying to view the Human to other Vertebrate genome >> comparisons listed here >> http://hgdownload.cse.ucsc.edu/downloads.html#human >> and I am wondering what is the best way to view these .net and/or .chain >> files. >> >> Thanks, >> Bryan >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
