Hi Alona, Sorry for the delayed response. There are a few ways to get this sequence. You can use the table browser to get all the rows from the MSA by selecting the Conservation track from the Comparative Genomics group, then select the relevant multiz table (multiz46way on hg19). The table browser lets you specify a region of interest in the "position" field. There's no way to filter out certain species using this mechanism.
Another way is to use the Conservation track controls to only show the species that you are interested in (you can get to the track controls by clicking on the title of the track, "Conservation", above the display selection pull-down menu). Once you have the species you are interested in, you can click on the alignment and copy/paste the MSA information off the resulting detail page. A third way is available if your sequence is within the coding sequence of a gene. To use this mechanism, choose your gene track (e.g. UCSC genes), set your region of interest, then choose "CDS FASTA from multiple alignment" in the output format pull down, then hit Submit. The next page that comes up will allow you to restrict the species that are output, as well as the formatting of the nucleotides. Keep in mind that restricting the display to only certain species does /not/ realign the data. Please let us know if you have any additional questions: [email protected] - Greg Roe UCSC Genome Bioinformatics Group On 4/30/12 4:37 AM, Alona Rabner wrote: > Hello, > > I've got a certain chromosome position (~ 400 bp) , and I'd like to > retrieve a Multiz alignment sequence for 10 vertebrates only (those, > I've chosen for better alignment) and in this certain area. Tables give > me position only. Is there any possible convenient way to retrieve this > certain Multiz alignment sequence , excluding the download of whole > genome MSA (8.3 Gb) ? > > Thank you, > Alona > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
