Dear Chuangye, If you don't want to use the table browser, you can download the source code to our browser (http://hgdownload.cse.ucsc.edu/downloads.html#source_downloads). The source code is free for academic, non-profit, and personal use.
>From the command line you can use our faFrag utility: $ faFrag faFrag - Extract a piece of DNA from a .fa file. usage: faFrag in.fa start end out.fa options: -mixed - preserve mixed-case in FASTA file For future reference here is a list all of our command line tools: http://genomewiki.ucsc.edu/index.php/Kent_source_utilities I hope this helps. Please contact the mailing list if you have further questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Chuangye" <[email protected]> To: [email protected] Sent: Friday, July 2, 2010 2:49:40 AM GMT -08:00 US/Canada Pacific Subject: [Genome] how to fetch sequence by mysql if provide bed files Dear Sir, Could you tell me how to use MySQL to download the corresponding sequence fasta files if provided bed format files as followings other than Table Browser? Thank you in advance. chr2 114334957 114336428 F379 + chr2 114320849 114320877 DQ598479 + chr2 114297628 114300242 AY343891 - Chuangye _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
