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PathwayAssist 2.0, FGENESH, Screener, Bioperl 1.2.3, Bioperl-Microarray

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Ariadne Genomics has released PathwayAssist 2.0, desktop software for visualization and analysis of cell signaling pathways, molecular networks, and protein-protein interaction data from experiments and literature. A free, 20-day trial is available at www.ariadnegenomics.com. PathwayAssist comes with a MedScan module for automated extraction of information from scientific literature, and ResNet, a molecular networks database compiled from Medline abstracts and other public data sources. New features include Build Pathway tools to find functional associations between genes derived from microarray experiments, and database importers for KEGG, BIND, DIP, and GO.


Softberry has released a new parameter set for gene annotation in fish, diatom, and Aspergillus genomes for its FGENESH ab initio gene prediction software at http://www.softberry.com/berry.phtml?topic=index&group=programs&subgroup=gfind.


Oak Ridge National Laboratory has released genes predicted using the GrailExp software program for NCBI human build 33 at http://compbio.ornl.gov/channel/index.html.


Genedata has released version 2.0 of its Screener software for high-throughput screening and pharmacological profiling data. The new release extends coverage of screening workflow by incorporating the analysis of hit confirmation screens, dose-response-, and high-content assays.


Bioperl 1.2.3 is now available at http://www.bioperl.org/Core/Latest/. The release contains minor functionality improvements and several bugfixes from the 1.2.2 release. The next set of developer’s releases for Bioperl, to be numbered 1.3.x, are planned for the fall of 2003.


The Bioperl project has also released version 0.1 of Bioperl-Microarray, an extension package for manipulating microarray data. It currently supports Affymetrix GeneChip CEL, CDF, Microarray Suite 5.0, and dChip files. Support is planned for Bio::MAGE objects and MAGE-ML, Affymetrix SNPChip genotype files, and GenePix GPR files for version 0.2. The release package is available at http://www.bioperl.org/DIST/.

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The Scan

Researchers Compare WGS, Exome Sequencing-Based Mendelian Disease Diagnosis

Investigators find a diagnostic edge for whole-genome sequencing, while highlighting the cost advantages and improving diagnostic rate of exome sequencing in EJHG.

Researchers Retrace Key Mutations in Reassorted H1N1 Swine Flu Virus With Avian-Like Features

Mutations in the acidic polymerase-coding gene boost the pathogenicity and transmissibility of Eurasian avian-like H1N1 swine influenza viruses, a PNAS paper finds.

Genome Sequences Reveal Evolutionary History of South America's Canids

An analysis in PNAS of South American canid species' genomes offers a look at their evolutionary history, as well as their relationships and adaptations.

Lung Cancer Response to Checkpoint Inhibitors Reflected in Circulating Tumor DNA

In non-small cell lung cancer patients, researchers find in JCO Precision Oncology that survival benefits after immune checkpoint blockade coincide with a dip in ctDNA levels.