Dear Vish, To get to the DNA sequence for the hg18 assembly you will need to select the hg18 assembly from the gateway page: http://genome.ucsc.edu/cgi-bin/hgGateway
After clicking "submit", click on "DNA" from the blue navigation bar. For each assembly that you are interested in getting DNA sequences, you will need to go through this process. Unfortunately, the get DNA tool doesn't have the ability to separate out the different classes of repeats. However, there is a way to get the sequence for low complexity repeats using the Table Browser. To get to the Table Browser click on "Tables" from the blue navigation bar. Set the following: Select the clade, genome, and assembly that you are interested in. group: Variations and Repeats track: RepeatMasker table: rmsk region: genome filter: click on "create". After "repClass does", paste in: 'Low_complexity' (to get this value click on "describe table schema" on the main table browser page for the table you are interested in.) Click "submit". output format: sequence click "get output" click "get sequence" This will give you the sequences of all of the low complexity repeats. Please feel free to contact the mailing list if you have further questions. Vanessa Kirkup Swing UCSC Genome Bioinformatics Group ----- Original Message ----- From: "Vishnu Mishra" <[email protected]> To: [email protected] Sent: Thursday, February 10, 2011 2:32:22 PM Subject: [Genome] Low complexity sequence The Get DNA in window function allows for identifying repeats by lower case or Ns. Is there a way to do the same for low complexity sequence filtering? Can they be highlighted or is there some other program to identify low complexity sequence? Also, the get DNA in window defaults to hg19. Is there a way to get DNA sequence for hg18. Thanks Vish Vishnu Mishra Senior Scientist, Diagnostic Assay Development Illumina, Inc. 9885 Towne Centre Drive San Diego, CA 92121 Tel: 858-246-8813 E-mail: [email protected]<mailto:[email protected]> _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
