Hello Marc, Using the tools at UCSC, the Table Browser will return blocks of Conservation MAF results, but not specific bases. However, by sending the data over to Galaxy, "slices" of the Conservation track's MAF alignment can be retrieved in batch using a custom track of intervals (down to a single base).
To do this: 1) Create and load a custom track in BED format of the genome positions of interest 2) Send the custom track to Galaxy by extracting it from the Table browser and checking Galaxy as the output choice 3) Send of the Conservation track's MAF alignment data to Galaxy using same method (you may need to subset this by chromosome to improve speed/performance) 3) Use the Galaxy tools: Fetch Alignments -> Extract MAF blocks given a set of genomic intervals UCSC help is as follows: http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#CustomTracks http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser http://genome.ucsc.edu/FAQ/FAQformat#format1 http://genomewiki.ucsc.edu/index.php/Coordinate_Transforms Galaxy help is available at their web site if you have questions about the tools. Thanks, Jennifer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Marc Yao" <[email protected]> wrote: > From: "Marc Yao" <[email protected]> > To: [email protected] > Sent: Sunday, January 10, 2010 8:09:23 AM GMT -08:00 US/Canada Pacific > Subject: [Genome] How to get corresponding bases in multiz alignment in a > high-throughput way? > > Dear Sir or Madam, > > I am working on the conservation between mouse genome and other > mammalian genomes. I wonder how I can extract corresponding target > genome sequences given mouse coordination as a query. For example, the > 30-way multiz alignment track in genome browser shows 'C' is at > chr4:139,328,937 in mouse genome and the corresponding base in rat > genome is 'T' and in human genome is 'G'. I have scores of thousands > of such queries need to make. Is there a way (or script/code) to do > this in a high-throughput way? > > Thanks, > > Marc > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
