Hello, The option #2 below works well for batch. Some simple scripting may be necessary on your part to extract the regions or you can experiment with the other maf* programs to see if they can get you to the BED file stage. Many rely on a database - which is available as a public mySQL server. http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities http://genome.ucsc.edu/FAQ/FAQdownloads#download29
Thanks, Jennifer Jackson UCSC Genome Bioinformatics Group ----- Original Message ----- From: "irix fun" <[email protected]> To: "Jennifer Jackson" <[email protected]> Cc: [email protected] Sent: Tuesday, July 21, 2009 10:24:05 AM GMT -08:00 US/Canada Pacific Subject: Re: [Genome] How to get the completed multiple-species alignment? Hi Jennifer, Thanks for your replying. Actually, I want to know whether there is any program can do it locally and easily like " mafsinRegion" which is provided by Kent. In other words, is any toolkit can get the whole alignment automatically instead of extracting the sequence by hand? Thanks again. Xiake On Tue, Jul 21, 2009 at 1:28 AM, Jennifer Jackson < [email protected] > wrote: Hello Xiake, Some easier ways to retrieve the genomic sequence (for any species): 1) Use the "Get DNA" tool in that species home browser. First adjust the browser window to the position, then submit and download. 2) Use the Table Browser. Either enter the coordinates in directly for a single location (using track Assembly, table gold) or create a custom track BED file to extract in batch (create/load custom track then open in TB). Select output as sequence for both methods. 3) Download the complete genomes from Downloads and extract using unix tools. Some help links: http://genome.ucsc.edu/FAQ/FAQdownloads#download1 http://genome.ucsc.edu/FAQ/FAQdownloads#download32 http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser http://genome.ucsc.edu/FAQ/FAQcustom http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks Since you already know the coordinates, this process should be fairly straightforward, but please let us know if you need more help or if we misunderstood your question. Thanks! Jennifer Jackson UCSC Genome Bioinforamtics Group ----- Original Message ----- From: "irix fun" < [email protected] > To: [email protected] Sent: Monday, July 20, 2009 8:09:06 AM GMT -08:00 US/Canada Pacific Subject: [Genome] How to get the completed multiple-species alignment? Hello, I am trying to get the multiple species alignment from "15-way insect alignment" locally. After parsing the result from lots of "MAF" file, I found that some indels exist in another species (not the reference species) but it's hard to get the sequence directly from "MAF" file. Does anybody get some ideas to solve this? Thanks very much. Xiake _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
