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
