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BioMart 0.6, Tripos Chemistry Extensions 1.0, KNIME, SXOligoSearch, Genbank 160.0

The European Bioinformatics Instituteand Cold Spring Harbor Laboratory have released BioMart version 0.6, which includes the DAS server, MartView, and MartBuilder. DAS server allows BioMart 0.6 to be used as a 1.5 DAS annotation server, configurable using standard BioMart configuration tools without requiring additional programming. MartView, viewable here, comes with an improved layout, better interactivity and quicker results panel response times for datasets with large configurations. The results come with a “unique rows” option. In addition to the existing web service XML button, MartView now features a Perl button that shows the query in Perl API format, and MartBuilder now allows one to execute, monitor and control transformation of SQL by remote. All code and documentation is available freely here.

Tripos has released Tripos Chemistry Extensions V1.0 for KNIME, the open-source workflow platform developed by researchers at the University of Konstanz, Germany. The new package introduces what the company calls “chemical intelligence” to the extensible KNIME platform, providing users with chemical structure manipulation, visualization, and other analysis features. By operating the new KNIME platform, Tripos customers now access software, open-source data-mining tools, and other third-party packages, the company said.

Synamatix has released SXOligoSearch, a new software application for mapping and analyzing reads from the Illumina-Solexa Genome Analyzer. The company said that SXOligoSearch offers 80 percent higher coverage, 104-fold faster mapping, and 14 percent higher sensitivity compared to Illumina’s ELAND mapping software
A free demo of SXOligoSearch is available here.

The National Center for Biotechnology Information has released GenBank 160.0 here. The release contains 77,248,690,945 base pairs and 73,078,143 entries. Uncompressed, the 160.0 flat files require about 280 GB for the sequence files only. The ASN.1 version requires around 237 GB. 

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