Hello Jeffery, Are you using the Table browser to search sequence text? Using the Table browser or mySQL to search long sequences with a regex is not recommended.
It would be much better to download the data and perform a search using your own tools locally (shell, perl). If you must use mySQL, the public server is likely a better place to build your own query (the Table browser may time out if the table is large, the text you are searching is long, and/or the search term is complex). Also, try using a REGEXP in the WHERE clause. REGEXP: http://dev.mysql.com/doc/refman/5.1/en/regexp.html For help, see the links 1, 2, 4 and the last on this FAQ page: http://genome.ucsc.edu/FAQ/FAQdownloads.html Jennifer --------------------------------- Jennifer Jackson UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 2/25/10 5:49 PM, Jeffrey Chao wrote: > Hi- > I would like to use a filter to search for a pattern that contains > some degenerate nucleotides. The basic query would be > seq LIKE '%ACG___G[ACG]CCC%' > When I try to use any filter that includes brackets for a range of > values, my search fails to find any sequences. Any advice you could > offer would be helpful. > Jeff > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
