Hello, For a large or compute intensive queries, it is recommended to download the data files and process queries locally.
If you need genome sequence for your regions, then downloading the genome sequence and extracting it using your own tools or a tool from our source tree is recommended. Genome sequence is not stored in the mySQL database. http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#Download If you are interested in obtaining track information (annotation) for these regions, then downloading the data tables and using a script (shell, perl) would be recommended. First, examine the tracks in the browser to find out which tables are associated (using the Table browser), then download the data from the Downloads server (species -> assembly -> Annotation database). Files with .txt.gz are the data and files with .sql are the schema. http://genome.ucsc.edu/FAQ/FAQdownloads.html#download1 http://genome.ucsc.edu/goldenPath/help/hgTracksHelp.html#TableBrowser You could always create your own mySQL database of just the data of interest and run SQL queries locally to extract information. You do not need to create an entire mirror to simply load a few files for your own use. Source & Utilities: Scroll to the second section, after the list of species, named Source Downloads: http://hgdownload.cse.ucsc.edu/downloads.html http://hgdownload.cse.ucsc.edu/admin/exe/ Description of Utilities: http://genomewiki.cse.ucsc.edu/index.php/Kent_source_utilities Jen --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/28/10 7:21 PM, OMER FARUK KUZU wrote: > Hi, > I am working on a project and need to use your database. > I require summary information for nearly 100000 small DNA sequences with a > average 10-15 base pairs. > What can I do. > I wish to use SQL but I dont know how to use it. And may be it will disturb > your servers. > What can I do? > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
