Krishna M Roskin
Affiliation: University of California
- Score functions for determining regional conservation in two-species local alignmentsKrishna M Roskin
Howard Hughes Medical Institute, Baskin School of Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA
J Comput Biol 11:395-411. 2004..We use them to get a very rough estimate of the amount of DNA in the human genome that is under selection...
- Meta-alignment with crumble and prune: partitioning very large alignment problems for performance and parallelizationKrishna M Roskin
Department of Computer Science, Univ of California, Santa Cruz, USA
BMC Bioinformatics 12:144. 2011..Both methods partition the problem such that many of the sub-problems can be solved independently. The results are then combined to form a solution to the full alignment problem...
- Aligning multiple genomic sequences with the threaded blockset alignerMathieu Blanchette
Howard Hughes Medical Institute, University of California at Santa Cruz, Santa Cruz, California 95064, USA
Genome Res 14:708-15. 2004..We describe our use of MULTIZ to produce the whole-genome multiple alignments at the Santa Cruz Genome Browser...
- The UCSC Table Browser data retrieval toolDonna Karolchik
Center for Biomolecular Science and Engineering, University of California Santa Cruz UCSC, School of Engineering, 1156 High Street, Santa Cruz, CA 95064 1077, USA
Nucleic Acids Res 32:D493-6. 2004..The Table Browser User's Guide located on the UCSC website provides instructions and detailed examples for constructing queries and configuring output...
- ENCODE whole-genome data in the UCSC genome browser (2011 update)Brian J Raney
Center for Biomolecular Science and Engineering, School of Engineering and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA
Nucleic Acids Res 39:D871-5. 2011..ENCODE data can also be retrieved using a metadata system that captures the experimental parameters of each assay. The ENCODE web portal at UCSC (http://encodeproject.org/) provides information about the ENCODE data and links for access...