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Beacon Designer, AKS v2.1, RefSeq 25, Aldente

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Premier Biosoft, developer of intuitive software for molecular biologists, has announced the release of a free edition of Beacon Designer, the company’s oligo design tool for real time PCR evaluation.
 
The software is used with SYBR Green primers and TaqMan primer/probe sets. It analyzes primers and probes for key characteristics including hairpins, dimers, runs and repeats, and calculates the Tm, GC percentage and length. The full version includes design support for all the popular real time PCR chemistries and is used in the laboratories around the world.
 
The release adds to the Premier Biosoft’s suite of tools including other free offerings: NetPrimer, a primer analysis program; and MutaPrimer, a desktop tool to design primers for Stratagene's QuikChange site-directed mutagenesis kits.
 

 
Active Motif, which offers research kits, assays and the TimeLogic biocomputing systems, has justreleased its AKS v2.1 from Bioalma. The latter was founded by scientists at the Spanish Research Council and is based in Madrid, Spain.
 
AKS 2.1, like its predecessor, allows users to uncover bioentity relationships that exist in over 8 million PubMed abstracts, but it now includes chemical information for millions of compounds and links to external databases such as PubChem. Additional functionality includes new internet subscription access, query alerts via e-mail, new export options, additional search options, new trend analyses, and enhanced graphical information.
 

 
The National Center for Biotechnology Information has released RefSeq 25 as part of its project to provide a curated, non-redundant collection of reference sequences, representative of the genomes, transcripts, and proteins for each major organism. This full release incorporates genomic, transcript, and protein data available as of Sept. 11, 2007, and includes 6,515,132 records, 4,167,224 proteins, and sequences from 4,646 different organisms.
 
The release is provided in several directories as a complete dataset and includes 4646 complete sets; 86 fungi, 294 invertebrate, 1283 microbes, 1224 mitochonidrion, 108 plants, 560 plasmids, 114 plastids, 83 protozoa, 228 vertebrate mammalians, 590 vertebrates, and 1,935 viral specimens.
 
The release is available for viewing here.
 

 
Geneva Bioinformatics and the Swiss Institute of Bioinformatics have released an enhanced version of Aldente, the peptide mass fingerprint tool developed by the SIB’s proteome informatics group.
 

This extended commercial version is available from GeneBio and builds upon the existing free version of Aldente accessible from the SIB’s ExPASy server. Further, it will allow users to use the software locally, thereby being able to upload proprietary sequence databases in a secured environment, and perform batch submissions, among other new features.

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