We mostly use C code around here. These options exist: 1. Execute an external utility like twoBitToFa 2. Develop a java-to-c interface to needed parts of kent source libraries 3. Try to translate twoBit library from C to java.
Also, you can just get the data such as knownGene from our downloads area in a variety of forms. You could either process the data directly as text dumps or load it into a database access it. -Galt > Hi, > > I have locally installed UCSC Genome Browser with main focus on mm8 assembly. > It is working fine and I can get all the sequences from 'Tables' browser > (based on KnownGene table gene's txStart and txEnd position information). But > I would like to extract these sequences programmatically (I am using Java and > 'mm8 database of Genome Browser' in my application development) for a given > knownGene entry (sequence between txStart and txEnd). How can I query the > mm8.2bit file to get those sequences for a given gene of knowGene table. > > Thanks, > Ashok > > > Ashok Reddy Dinasarapu Ph.D > University of California,San Diego > Department of Bioengineering > 9500 Gilman Drive, m/c 0412 > La Jolla, CA 92093-0412 > > > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
