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Raptor version 2.0, Genome Reviews 1.0, Ensembl 21, Prot_map, Paracel Blast 1.6, CCP4 5.0, Rfam 6.0, UCSC Genome Browser, FinchTV, SNOMED CT, HapMap data release 7

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Bioinformatics Solutions has released version 2.0 of its Raptor protein structure prediction software. The updated version uses linear programming to perform threading-based structure prediction, and uses NMR constraint data to improve accuracy, the company said.


The European Bioinformatics Institute has launched Genome Reviews 1.0 (http://www.ebi.ac.uk/GenomeReviews), a database of sequenced genomes for 153 prokaryotic organisms cross-referenced to other resources such as UniProt, the GOA GO annotation database, or InterPro.


Ensembl 21 is available at http://www.ensembl.org. The release includes an update for the human gene build, a new gene build for Fugu, an annotated assembly for chimpanzee, and an “experimental” text-mining resource called HUGO_text for mining Medline for HUGO symbols.


Softberry has released Prot_map, a tool for aligning proteins with a genome to reconstruct exon-intron structure, at http://sun1.softberry.ru/berry.phtml?topic=prot_map&group=programs&subgroup=xmap.


Paracel has released Paracel Blast 1.6 with native support for 64-bit AMD Opteron, along with its turnkey BlastMachine2 cluster with AMD64 processors.


Version 5.0 of the CCP4 suite of programs for macromolecular crystallography is now available at http://www.ccp4.ac.uk/download.php. New features include a module to extend Fourier maps and compute the standard uncertainty of electron density; coordinate utility programs based on the MMDB library; and programs for extracting deposition data from PDB logfiles.

New features include a module to extend Fourier maps and compute the standard uncertainty of electron density; coordinate utility programs based on the MMDB library; and programs for extracting deposition data from PDB logfiles.


Rfam 6.0, a database of multiple alignments and covariance models of 350 non-coding RNA families, is available at http://rfam.wustl.edu/.


The University of California Santa Cruz genome bioinformatics group has released a Genome Browser and Blat server for the March 2004 assembly of the C. elegans genome at ftp://genome.ucsc.edu/goldenPath/ce2/.


Geospiza has upgraded its FinchTV chromatogram-viewing utility to include printing capabilities and support for exporting Fasta files. The software is freely available at www.finchtv.com.


SNOMED CT (Systematized Nomenclature of Medicine Clinical Terms) is now available as part of the National Library of Medicine’s Unified Medical Language System Metathesaurus at http://umlsks5.nlm.nih.gov/kss/servlet/Turbine. Users must register for a free UMLS license before downloading the Metathesaurus.


HapMap data release 7 is available from the HapMap Data Coordination Center at Cold Spring Harbor Laboratory at http://www.hapmap.org. The release contains 50,137,470 genotypes. Frequencies, genotypes, and assays can be downloaded in bulk from http://www.hapmap.org/downloads/.

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The Scan

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.

Circulating Tumor DNA Linked to Post-Treatment Relapse in Breast Cancer

Post-treatment detection of circulating tumor DNA may identify breast cancer patients who are more likely to relapse, a new JCO Precision Oncology study finds.

Genetics Influence Level of Depression Tied to Trauma Exposure, Study Finds

Researchers examine the interplay of trauma, genetics, and major depressive disorder in JAMA Psychiatry.

UCLA Team Reports Cost-Effective Liquid Biopsy Approach for Cancer Detection

The researchers report in Nature Communications that their liquid biopsy approach has high specificity in detecting all- and early-stage cancers.