Good Afternoon: Translate your coordinates to bed file format: sed -e "s/:/ /; s/-/ /;" yourFile.txt > yourFile.bed
Input that bed file as a custom track to the genome browser: http://genome.ucsc.edu/goldenPath/help/customTrack.html Use the table browser to extract your custom track in sequence format: http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html --Hiram ----- Original Message ----- From: "vaibhav jain" <[email protected]> To: [email protected] Sent: Tuesday, December 28, 2010 10:50:56 AM Subject: [Genome] Query related to retrieving DNA sequences Respected sir/madam Thanks a lot for replying for my previous queries. But I have one more query, I have chromosome locations of certain genes and I want to retrieve their DNA sequences. Example of some of the locations are as follows: chr14:35428126-35429126 chr15:42529569-42530569 chr3:136753204-136754204 chr6:128538865-128539865 chr13:96441628-96442628 chr10:43435933-43436933 chr10:92078555-92079555 chr8:115357078-115358078 chr14:33161142-33162142 chr14:12744634-12745634 chr20_random:7264-8264 chr8:11555485-11556485 chr20:1628167-1629167 chr2:31591784-31592784 chr2:24596869-24597869 chr14:35428126-35430126 chr15:42529569-42531569 One way of retrieving sequence which I know is by retrieving sequence one by one from the DNA track of the UCSC, but I want to know if there is a way through which we can retrieve all the sequences for all the locations together. Thanks and regards Vaibhav Jain Research Scholar @IGIB New Delhi, INDIA _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
