, 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
. 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.
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.
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.
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.”