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MapEditor, MetaLink, BioWorks 3.3, lpgLIMS 1.3, Blast 2.2.15

GeneGo has launched MapEditor and MetaLink, add-on modules for the company’s MetaCore software designed for integrating, editing, and mapping custom interaction data. MapEditor allows users to generate custom pathway maps, converting a network into a pathway map, or edit one of the existing 500 proprietary maps from MetaCore. MetaLink allows users to batch-upload their own protein association data produced by yeast-two-hybrid screens, gene co-expression, pull-down assays, text mining and other methods in MetaCore and build networks on the fly.

Thermo Electron has released BioWorks 3.3, an updated version of its protein analysis software package that enables automated quantitative analysis of iTRAQ-, SILAC-, and ICAT-labeled samples, as well as label-free quantitation techniques. BioWorks 3.3 includes a new probability-based scoring algorithm for protein identification, as well as a unified “Search Results File” feature that allows all of the information to be stored in a single file. It also includes enhanced queue and batch search capabilities for its Sequest package, which will enable users to launch searches on Matrix Science’s Mascot server from Bioworks and compare Sequest and Mascot search results.

The National Cancer Institute’s Cancer Biomedical Informatics Grid project has released lpgLIMS 1.3, an enhanced version of caLIMS 1.2, here. lpgLIMS includes new adapters for Applied Biosystems’ 3100 and 3730XL sequencers and Affymetrix’s 10K, U133A, U133B and U133plus2 GeneChips. It has been tested on Windows, Linux, and Solaris.

Blast 2.2.15 is available from the National Center for Biotechnology Information here. Blast now uses a 28-letter protein alphabet supporting the J (leucine or isoleucine) and O (pyrrolysine) residues. In addition, megablast now supports incremental ASN.1 output and Blast binaries are available for Windows XP/2003 x64 edition.

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The Scan

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Additional Genes

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Science Papers Examine State of Human Genomic Research, Single-Cell Protein Quantification

In Science this week: a number of editorials and policy reports discuss advances in human genomic research, and more.