Hello Rad, You will want to use the table browser. Go to http://genome.ucsc.edu/cgi-bin/hgTables, choose your assembly of interest and then select:
group: Comparative Genomics track: Conservation table: You will want one of the conserved elements tracks (i.e. Mammal El or Vertebrate El) region: click on "define regions" This will take you to a menu where you can input your bed formatted coordinates. Then you can select: output format: "all fields from selected table" or "selected fields from primary and related tables" depending on which fields you wish to retrieve from this table. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu On 11/28/11 1:28 PM, Mohamed Radhouane Aniba wrote: > Hello everyone, > > I have a bed file containing some genomic features with coordinates > > I would like to extract automatically two information concerning the UCSC > conservation (hg18 vertebrate) : > > Number of Conserved bases (coverage basically) > Number of conserved blocks (corresponding to these bases) > I remember there is a ucsc tool that do that but I lost its name, any idea ? > > Thanks > > Rad > > > Radhouane Aniba > Bioinformatics Postdoctoral Research Scientist > Institute for Advanced Computer Studies > Center for Bioinformatics and Computational Biology (CBCB) > University of Maryland, College Park > MD 20742 > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
