Hello, Varun. You can do most of what you describe with the Table Browser. If you're unfamiliar with the Table Browser, you can see the Table Browser User's Guide at http://genome.ucsc.edu/goldenPath/help/hgTablesHelp.html.
Let's assume you wanted to get the length of the coding sequences of chromosome 21 of the RefSeq Genes track of the human genome (hg19). In the blue navigation bar at the top, click "Tables" which will take you to the Table Browser. Then you would set the following: clade: Mammal genome: Human assembly: Feb. 2009 (GRCh37/hg19) group: Genes and Gene Prediction Tracks track: RefSeq Genes table: refGene region: chr21 output format: selected fields from primary and related tables It sounds like you already have a list of genes you'd like to work with. If that is the case, you can click the "paste list" or "upload list" button next to "identifiers" to use your own custom set of genes. Then click the "get output" button which will take you to a new screen where you can select the fields you are interested in. For your question, you would probably want to select something like: name cdsStart cdsEnd name2 You can obviously select whatever you want from the list based on your preferences. Then click the "get output" button which will display your results. This will give you the start and stop positions of the coding regions, but not the length. To get the length, you would need to put these results into another program like Excel where you can create a formula that would give you the lengths based on the start and stop positions. Please contact us again at [email protected] if you have any further questions. --- Steve Heitner UCSC Genome Bioinformatics Group -----Original Message----- From: [email protected] [mailto:[email protected]] On Behalf Of varun gupta Sent: Tuesday, November 01, 2011 8:12 AM To: [email protected] Subject: [Genome] Orf Length Hi EveryOne I ahve a simple question. If i have a set of genes can i get their orf length(i mean length of the Coding sequences) Hope to hear from you soon Regards Varun _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
