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RNA_MAP, SBML, BlastMachine, dnatools


Softberry’s new RNA_MAP RNA/EST mapping program is now available at scan.html.

RNA_MAP is an algorithm to accurately map mRNA sequence to genomic sequence while taking into account splice sites flanking intron sequences.

Softberry, based in White Plains, NY, also offers EST_SMAP for mapping the whole set to a chromosome sequence and OLIGO_MAP to map a set of oligonucleotides used for microarray production.

The final specification for Level 1 of SBML (the systems biology markup language) is available from

SBML is an XML-based description language for simulations in systems biology. It was developed by researchers at Japan’s ERATO Kitano Systems Biology Project and the California Institute of Technology.

Paracel, a Pasadena, Calif.-based business unit of Celera Genomics, has released its BlastMachine system, a software and hardware solution that executes Paracel’s optimized versions of the National Center for Biotechnology Information’s Blast algorithm. BlastMachine runs blastn, blastp, blastx, tblastn, and tblastx.

The Paracel Filtering Package (PFP), a cleaning, filtering, and masking utility for DNA and protein sequence data, is included with the purchase of a BlastMachine system.

Version 5.2.001 of dnatools, a software package for sequence management and analysis developed by the department of yeast genetics at the Carlsberg Research Center, is available at

Improvements include revised EST clustering functions and improved handling of multi-sequence files.

Filed under

The Scan

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Arranged Killing, Fraud Alleged by Prosecutors

The Wall Street Journal reports that prosecutors allege that the co-founder of a biotech arranged to have a business associate who threatened to expose him as a fraud killed.

Whirlwind Decade of CRISPR

The New York Times looks back at the 10 years since the University of California, Berkeley's Jennifer Doudna and her colleagues published their CRISPR paper.

PNAS Papers on Blue Cone Monochromacy Structural Variants, HIV-1 Mutant, T-ALL

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