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NextGENe, HIV Data Browser, UCSC Genome Browser, Expressionist 5.0

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SoftGenetics has released NextGENe, a software package for next-generation sequencing. NextGENe’s applications include de novo and target assembly, SNP/Indel discovery, digital gene expression analysis, ChIP-seq, transcriptome analysis using cDNA, and miRNA discovery and quantification, the company said.
 
The software runs on 54-bit Windows systems.
 
Jonathan Liu, vice president of development at SoftGenetics, said that the software includes a “condensation tool” that can reduce “instrumental and other errors” by 10 percent.
 
The company is offering free 30-day trials of the program.
 

 
Global Solutions for Infectious Diseases has launched the HIV Data Browser, which includes clinical and viral sequence data from infected subjects in the VAX004 Phase III clinical trial of the AIDSVAX B/B vaccine.
 
The browser, which is a customized version of the UCSC Genome Browser developed by the Genome Bioinformatics group at the University of California, Santa Cruz, and hosted by GSID, includes searchable demographic and clinical data from volunteers who became HIV infected during the VAX004 trial.
 
Future releases will include the addition of clinical and viral sequence data from infected subjects in the VAX003 Phase III clinical trial of AIDSVAX B/E, and immunogenicity data from infected subjects in both the VAX004 and VAX003 trials.
 

 
Genedata has released Expressionist 5.0. Thelatest version of the company’s enterprise high-throughput biomarker discovery platform includes classification tools such as ROC curves and k-fold cross validation; the ExpressMap module for cross-validation of expression data from different platforms or comparison of treatment effects in different samples; a Gene Ontology browser; and correlation networks that describe relationships between individual groups of genes, proteins, or metabolites.

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The Scan

Omicron's Emergence

The World Health Organization has called Omicron a SARS-CoV-2 "variant of concern," the Los Angeles Times writes.

Not as Much

Merck's pill to treat COVID-19 reduces the risk of hospitalization and death among COVID-19 patients by less than previously reported, the New York Times says.

Bats That Hang Together

Discover magazine writes that researchers have found a social microbiome among vampire bats.

PLOS Papers on CEWAS, Simian Varicella Virus Transcriptome, Dermatomyositis Markers

In PLOS this week: multi-omic approach to home in on genetic risk variants, transcriptomic analysis of the simian varicella virus, and more.