Good Morning Abrita: We do not keep genome sequence in the MySQL database.
There are several alternatives you can use to fetch lots of sequence. The most efficient method would be to use the 2bit file for the assembly of interest, and the kent source program twoBitToFa which can rapidly extract sequence from the 2bit file given a set of coordinates. The hg18 assembly 2bit file can be fetched from: http://hgdownload.cse.ucsc.edu/goldenPath/hg18/bigZips/ The twoBitToFa program can be fetched from: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ An alternative to that is to place all your coordinates into a single bed file, submit that file as a custom track into the genome browser, then use the table browser to download that track in fasta format. --Hiram abrita chakravarty wrote: > Hi, > Could you please let me know the name of the table I could use to > download a gene sequence from, given the co-ordinates? > > Currently I can do this from the Table Browser graphical interface. > However I would like to automate the process using a script that > connects to the mysql database genome-mysql.cse.ucsc.edu and executes > a mysql query to download the sequence. > > Thank you, > Sincerely, > Abrita Chakravarty _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
