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Bioinformatics-related methods


Bioinformatics-related methods are featured in Cold Spring Harbor Protocols

COLD SPRING HARBOR, N.Y. (Mon., July 2, 2007) – Large-scale undertakings such as the Human Genome Project have produced massive amounts of data. To make sense of it all, powerful mathematical and statistical algorithms were developed, resulting in the interdisciplinary field called “bioinformatics.” By probing genome sequence data with in silico tools, biologists can infer the functions of specific genes, evaluate the evolutionary relatedness among species, and identify DNA variants that are predictive of disease. This valuable information can both complement and drive the more traditional laboratory-based experimental studies. This month’s release of Cold Spring Harbor Protocols highlights two articles that discuss the principles and applications of cutting-edge bioinformatics software programs; both are freely available online (cshprotocols.cshlp.org).

The first freely available article (cshprotocols.cshlp.org/cgi/content/full/2007/14/pdb.top17) provides guidance on how to use the BLAST (Basic Local Alignment Search Tool) program. BLAST is the tool that is most commonly used to search large databases for DNA and protein sequences with similarities. The article, intended to be a “user’s guide” to BLAST, includes a general overview of its algorithmic basis as well as descriptions of various BLAST programs and their appropriate applications. It will be useful to a wide range of biologists seeking to better understand and apply BLAST to their systems.

The second freely available article describes a computational pipeline that has been optimized to identify DNA variants called SNPs (single-nucleotide polymorphisms) in sequence data from corn. The sequences, generated with cutting-edge technology from 454 Life Sciences, are aligned and anchored to the corn genome using BLAST and cross_match (another computational tool). Then, a third program called PolyBayes is used to search for SNPs in the aligned sequences. The article describing this SNP-discovery pipeline is available at (cshprotocols.cshlp.org/cgi/content/full/2007/14/pdb.prot4786).

For a complete list of all articles in the July release of Cold Spring Harbor Protocols, please see (cshprotocols.cshlp.org/TOCs/toc7_07.dtl).


Cold Spring Harbor Protocols (cshprotocols.cshlp.org) is an online resource of methods used in a wide range of biology laboratories. It is structured to be highly interactive, with each protocol cross-linked to related methods, descriptive information panels, and illustrative material to maximize the total information available to investigators. Each protocol is clearly presented and designed for easy use at the bench—complete with reagents, equipment, and recipe lists. Life science researchers can access the entire collection via institutional site licenses, and can add their suggestions and comments to further refine the techniques.

Cold Spring Harbor Laboratory Press is an internationally renowned publisher of books, journals, and electronic media located on Long Island, New York. It is a division of Cold Spring Harbor Laboratory, an innovator in life science research and the education of scientists, students, and the public. For more information, visit www.cshlpress.com.

For content and submission information:
David Crotty (crotty@cshl.edu; 516-422-4007), Executive Editor, Cold Spring Harbor Protocols

For access, subscription, and free trial information:
Wayne Manos (manos@cshl.edu; 516-422-4009), Director, Serials Marketing, CSHL Press

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