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mpiBlast, DNAStar s Lasergene 6, John Innes Center and Affymetrix, OpenEye Scientific Software s Ogham and LexiChem, Infotrieve s Infotrieve/ELN 2.4, and Nucleic Acids Research

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An updated version of mpiBlast, a parallelized version of NCBI Blast, is expected to be released next week, Aaron Darling of the University of Wisconsin-Madison, the lead developer for the software, told BioInform at ISMB last week. The new release, version 1.4, offers a 350-fold speed-up over NCBI Blast on a 128-CPU cluster, Darling said. The software is available at http://mpiblast.lanl.gov/.


DNAStar has released an updated version of its Lasergene 6 sequence analysis software to support Mac OS X Tiger (10.4). Lasergene 6 Mac users who have upgraded to OS 10.4 can download and install the Lasergene Tiger update at https://www.dnastar.com/web/login.php.


The John Innes Center in Norwich, UK, has released an Affymetrix expression module for its Genome Laboratory Information Management System (GenomeLIMS). The system is free for academic researchers at http://www.jicgenomelab.co.uk/jgl/microarrays_workflow.php. GeneChip customers can use the system to submit and track samples through the expression workflow from initial sample QC using the BioAnalyzer to final data QC from the Affymetrix report files. Sample information is automatically parsed into the GCOS expression format.


OpenEye Scientific Software has released Ogham and LexiChem, programs for 2D rendering, compound naming, and the generation of structures from names. Ogham renders 2D drawings from 3D structures or connectivity information. LexiChem converts chemical names into chemical structures and vice versa. Both products are available either as standalone applications or as C++ toolkits for in-house or third-party software-development purposes.


Infotrieve has released Infotrieve/ELN 2.4, an electronic laboratory notebook enterprise software package. The product is built on the GenSys/ELN, which Infotrieve acquired in its purchase of GenSys software in December 2004.


Nucleic Acids Research has published its annual web server issue, which includes 159 papers describing 166 web-based computational tools for analyzing DNA, RNA, and protein sequences and structures. The issue is freely available to subscribers and non-subscribers at http://nar.oxfordjournals.org/content/vol33/suppl_2/index.dtl?etoc. A complete listing of the 2005 NAR servers is available at http://bioinformatics.ubc.ca/resources/links_directory/narweb2005/.

 

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