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Merops-Pro, PepSea, NetAffx, Pyrosequencing, SSAHA

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BioWisdom of Cambridge, UK, has released version 1.3 of the Merops-Pro protease database, which is incorporated into BioWisdom’s Discovery Portfolio platform. New features of Merops-Pro 1.3 include the addition of 60,000 human and mouse ESTs, more informative EST data cards, the inclusion of links to LocusLinks at NCBI, and an improved downloads table.

BioWisdom has also added new peptides to Discovery Portfolio. The peptides have been designed by Proteom to bind with a broad range of proteins, including G-protein coupled receptors, ion channels, kinases, and proteases.

 

Toronto-based MDS Proteomics has added the PepSea protein identification tool to its bioinformatics offerings. PepSea allows users to identify unknown proteins and to determine the location and identity of human genes that encode the proteins. According to MDS, the error-tolerant PepSea algorithm enables proteins to be identified regardless of “junk” DNA and introns, which make up the majority of human DNA.

 

Affymetrix of Santa Clara, Calif., has launched its NetAffx website (www.netaffx.com), which integrates the data generated by Affymetrix’ GeneChip arrays with biological information from public and private databases. Users can also use NetAffx to choose genes or groups of genes to design GeneChip CustomExpress probe arrays.

 

SNP Primer Design software now available from Uppsala, Sweden-based Pyrosequencing enables researchers to design primers that are optimized for use with Pyrosequencing’s DNA analysis technology. The Web-based assay design tool is able to evaluate and select primers tailored for use with Pyrosequencing’s PSQ 96 and PTP systems. Registered Pyrosequencing users can download the software through the tech support area of www.pyrosequencing.com.

 

The Sanger Center has released version 2.0 of SSAHA (Sequence Search and Alignment by Hashing Algorithm) for matching and alignment of DNA and protein sequence data. According to its developers, SSAHA can search human-genome-sized databases approximately three orders of magnitude faster than Blast.

The new version provides a percentage identity for each match as well as better handling of gaps and tandem repeats.

SSAHA 2.0 is available for download at www.sanger.ac.uk/Software/analysis/SSAHA. In addition, the software is available to search against the latest human “golden path” assembly at www.ensembl.org/ perl/ssahaview or against the Ensembl Trace Repository at http://trace. ensembl.org/perl/ssahaview.

 

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