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Downloads & Upgrades: Dec 19, 2008

GPU-HMMER, a port of HMMer's hmmsearch utility to nVidia GPUs that have been enabled with the company’s Compute Unified Device Architecture, or CUDA, is available here.  
GPU-HMMER was developed as a collaboration between researchers at Wayne State University, University at Buffalo, and Scalable Informatics.
According to the developers, GPU-HMMER has been tested on 8800 GTX Ultra and Tesla C1060 GPUs and it has demonstrated speedups exceeding 100-fold using 3 Tesla GPUs, depending on the size of the HMM.

Symyx Technologies has released Symyx Assay Explorer 3.2. The latest version of the biological information management system allows users to query data across experiments and search for specific variables within experiments; analyze time series and dose response curves; report curves and data together in Excel spreadsheets; and apply new experiment templates for rapidly initiating workflows.
Symyx Assay Explorer 3.2 supports Microsoft Windows XP SP2, XP SP3, Vista SP1, and Office 2007 SP1.

The National Center for Biotechnology Information has released Blast 2.2.19. Binaries are available here.
NCBI said that the BLASTDB environment variable now supports multiple database search paths and that a smaller protein lookup table is used to improve performance when possible. The new release also includes several bug fixes.

NCBI has also released GenBank 169.0 via FTP. It contains data as of Dec. 11. The new release comprises approximately 99.1 gigabases of data and 98.9 million entries from non-WGS, non-CON sequences; and 141.4 gigabases of data and 48.4 million entries from WGS sequences. 
Uncompressed, the 169.0 release flatfiles require about 381 GB for sequence files only. The ASN.1 data require approximately 349 GB.

UniPro has released UGENE 1.3, a free software package for integrating molecular biology tools within a single graphical environment. Version 1.3 includes three new plug-ins: Workflow Designer, which allows users to create and run custom computational workflows; SITECON, which searches for transcription factor binding sites in DNA sequences; and BioStruct3D, a 3D molecular protein and DNA structure viewer for the PDB format.

Transinsight has launched GoPubMed 4.0. According to the company, GoPubMed 4.0 is 10 times faster than the previous version of the biological search engine, and can handle “millions of documents in seconds.” The new version also includes an interactive filtering process that “reduces millions of documents to a handful of key papers in just a few clicks,” and a Web 2.0 query processor that suggests search ideas as users type, the company said.

Qlucore has launched Qlucore Gene Expression Explorer, a software platform that presents all data sets in 3D “so that researchers can easily visualize them in real-time, directly on the computer screen,” the company said. It allows users to analyze and explore data sets of up to 100 million samples on a PC.

The company said that the software can be used to study gene expression microarray data, protein array data, miRNA data, RT-PCR data, protein data from 2D gels, and “any data set of multivariate data of sizes up to 1,000 samples and 100,000 variables, or 1,000 variables and 100,000 samples.”

Filed under

The Scan

US Booster Eligibility Decision

The US CDC director recommends that people at high risk of developing COVID-19 due to their jobs also be eligible for COVID-19 boosters, in addition to those 65 years old and older or with underlying medical conditions.

Arizona Bill Before Judge

The Arizona Daily Star reports that a judge weighing whether a new Arizona law restricting abortion due to genetic conditions is a ban or a restriction.

Additional Genes

Wales is rolling out new genetic testing service for cancer patients, according to BBC News.

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.