Hello, Data can be accessed through the mySQL server, the Table browser (useful for determining file format and linked relationships), and our ftp Download area. If you want to write your own mySQL query for batch, custom output, use our public mySQL server. For any complete table/files, use ftp. To understand the contents of a file and any related files, use the Table browser (drill down from assembly to track to table and click on "view table schema").
The Table browser can also be used to extract small regions of sequence easily as well as conservation data based on genomic positions. In short, the method is to upload a BED file of genomic coordinates and save output as fasta sequence, primary file data and/or related file data). Some links to FAQ/Help docs for using these tools: http://genome.ucsc.edu/FAQ/FAQdownloads#download1 http://genome.ucsc.edu/FAQ/FAQdownloads#download29 http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html A description of how the conservation track was generated (including the handling of repeat regions from native and comparative genomes), please see the Conservation track's description page. The processing has multiple steps to maximize coverage over challenging regions (such as repeats). Thank you, Jennifer Jackson UCSC Genome Bioinformatics Group Pete Shepard wrote: > Dearest Browser, > > I am trying to find all Vertebrate conserved elements for certain sections > of the genome, Along with these elements, I would like to get their > sequence. Am I able to write a mysql script to accomplish this as I have > quite a few sections I am interested in. Also, are repeat elements included > in the conservation track? > > > Thanks > _______________________________________________ > Genome maillist - [email protected] > http://www.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] http://www.soe.ucsc.edu/mailman/listinfo/genome
