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JAFA, eHiTS 5.3, Geneious 0.09, Cytoscape 2.2, EMBL Nucleotide Sequence Database, MView 1.49, Darwin LIMS, SDK 1.03, CNAT, and more


The Burnham Institute for Medical Research has released JAFA (Joint Assembly of Functional Annotation), a function prediction meta-server that accepts a protein sequence, queries several function prediction servers, and presents the results. JAFA is available at

SimBioSys has released eHiTS 5.3, an upgrade of its flexible ligand docking tool that automatically detects binding sites and evaluates all possible protonation states of the ligand and receptor in a single run. The new release uses the temperature factors included in PDB files to create a set of statistically derived empirical scoring functions that result in a far more accurate docking algorithm, according to the company. The software is free to academic users. Further information is available at

Biomatters has released Geneious 0.09 beta, a software system for searching and filtering DNA, protein, and publication data. The software is freely available at Features include a user interface for searching, sorting, and storing biomolecular sequence data and scientific publications, including the following features; a local database to store sequences and publications; direct links to Google scholar, NCBI, and UniProt; and rapid sequence similarity searching. Biomatters said it plans to release version 1.0 of Geneious in "early 2006."

Cytoscape 2.2 is available at The open-source platform for visualizing molecular interaction networks and integrating these interactions with gene expression profiles and other state data. New features include improved node/edge attribute browsing and editing; Cytoscape Graph Editor v1.0; support for loading Gene Ontology OBO and gene annotation association files; and improved performance.

Release 85 of the EMBL Nucleotide Sequence Database is available from (UK) and mirror sites. The file size is about 57.7 GB (compressed), and 320 GB (uncompressed).

MView 1.49, a tool for converting the results of a sequence database search into the form of a multiple alignment of hits stacked against the query, is available at

Thermo Electron has released Darwin LIMS, a laboratory information management system for pharmaceutical manufacturing R&D and QA/QC. Capabilities include dissolution, content uniformity, stability management, product management, batch management, and system interfacing. Darwin is built on the Microsoft .NET framework, which enables users to extend the system using industry-standard tools, the company said.

Affymetrix has released has released several updates through the Affymetrix Developer Network: Fusion SDK 1.03, which includes new interfaces to the CEL and CHP parsers and updates to the Java implementation, is available at; CNAT (Copy Number Analysis Tool) 3.0, which was designed to streamline the Affymetrix copy number analysis workflow, is available at; and GSEQ (GeneChip Sequence Analysis Software) 4.0, "an evolution" from GeneChip DNA Analysis Software 3.0 that was developed specifically to support the launch of the new CustomSeq Resequencing Array and Human Mitochondrial Array 2.0, is available at

The Genome Bioinformatics Group at the University of California, Santa Cruz, has released the latest mouse genome assembly from the Mouse Genome Sequencing Consortium, NCBI Build 35 (UCSC version mm7), through the UCSC Genome Browser. The assembly includes around 2.6 Gb of sequence, of which about 2.2 Gb is finished sequence. Sequence and annotation are available at and UCSC has also updated the dog Genome Browser to include the May 2005 v2.0 assembly (UCSC version canFam2) sequenced and assembled by the Broad Institute and Agencourt Bioscience. The dog sequence and annotation data are available at and

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The Scan

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