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ToxShield Suite 1.0, HapMap 15, SCOP 1.67, EMBOSS 2.10.0, BIND 3.7, GenBank 146.0, UCSC Genome Browser, BioBrew 3.1, BioMart version 0.2, CE-MC 1.1

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Gene Logic has launched ToxShield Suite 1.0, a web-based software platform for rank-ordering candidate drug compounds based on potential toxicities in humans. The software is based on predictive toxicogenomics studies that Gene Logic has performed for pharmaceutical clients.


HapMap 15 is now available at http://www.hapmap.org. Over a million SNPs have now been genotyped in all four HapMap populations.


SCOP (Structural Classification of Proteins) 1.67 is available at http://scop.mrc-lmb.cam.ac.uk/scop. It includes 24,037 PDB entries and 65,122 domains.


EMBOSS 2.10.0 has been released at ftp://ftp.rfcgr.mrc.ac.uk/pub/EMBOSS/ and http://emboss.sourceforge.net. The release corrects alignment numbering for some alignment formats and offers faster feature-table handling.


The Blueprint Initiative has released version 3.7 of the Biomolecular Interaction Network Database (BIND), at http://bind.ca/.


GenBank 146.0 is now available from the National Center for Biotechnology Information at ftp://ftp.ncbi.nih.gov/. The release contains 46,849,831,226 base pairs and 42,734,478 entries. Uncompressed, the 144.0 flat files require about 162 GB for the sequence files only. The ASN.1 version requires around 140 GB.


The University of California Santa Cruz Genome Bioinformatics Group has released a Genome Browser and Blat server for the September 2004 Btau_1.0 draft assembly of the cow genome, and a Genome Browser for a second honeybee assembly, Amel_2.0 (UCSC version apiMel2).


BioBrew 3.1, an open source Linux cluster distribution based on the NPACI Rocks cluster software that is enhanced for bioinformaticists and life scientists, is available at http://bioinformatics.org/biobrew/. The release includes updated versions of HMMer, Gromacs, EMBOSS, NCBI Blast, mpiBlast, Phylip, and mrBayes.


Ensembl has released BioMart version 0.2, which includes improvements designed to facilitate external installations, at http://www.ebi.ac.uk/biomart/install.html.


CE-MC 1.1, a software package for multiple protein structure alignment, is available at http://cemc.sdsc.edu/html/download.html. The standalone version of the software includes new features for generating output files containing transformed coordinates before and after structure alignment.

 

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The Scan

Interfering With Invasive Mussels

The Chicago Tribune reports that researchers are studying whether RNA interference- or CRISPR-based approaches can combat invasive freshwater mussels.

Participation Analysis

A new study finds that women tend to participate less at scientific meetings but that some changes can lead to increased involvement, the Guardian reports.

Right Whales' Decline

A research study plans to use genetic analysis to gain insight into population decline among North American right whales, according to CBC.

Science Papers Tie Rare Mutations to Short Stature, Immunodeficiency; Present Single-Cell Transcriptomics Map

In Science this week: pair of mutations in one gene uncovered in brothers with short stature and immunodeficiency, and more.