Skip to main content
Premium Trial:

Request an Annual Quote

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

Premium

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.

 

Filed under

The Scan

Study Reveals Details of SARS-CoV-2 Spread Across Brazil

A genomic analysis in Nature Microbiology explores how SARS-CoV-2 spread into, across, and from Brazil.

New Study Highlights Utility of Mutation Testing in Anaplastic Thyroid Cancer

Genetic mutations in BRAF and RAS are associated with patient outcomes in anaplastic thyroid carcinoma, a new JCO Precision Oncology study reports.

Study Points to Increased Risk of Dangerous Blood Clots in COVID-19 Patients

An analysis in JAMA Internal Medicine finds that even mild COVID-19 increases risk of venous thromboembolism.

Y Chromosome Study Reveals Details on Timing of Human Settlement in Americas

A Y chromosome-based analysis suggests South America may have first been settled more than 18,000 years ago, according to a new PLOS One study.