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Downloads & Upgrades: SeqSolve 2.1; TopHat 1.4.0; Genedata Screener 10; PhytoPath; Explore; RefSeq 51; and Others

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This week, Integromics released SeqSolve 2.1, the newest version of its software for next-generation sequencing data analysis.

According to the company, the release includes a scalable server mode that lets users set up and run multiple analyses, try different software settings, and perform several data comparisons. It also lets researchers access the data and set up analysis remotely.


This week, the developers of the GeneMania plugin for Cytoscape announced a new data release for the tool.

The group said that it has added iRefIndex as a replacement to the Pathway Commons data source for physical interactions, and it has changed the approach used to infer co-expression interactions, among other updates.


The Center for Bioinformatics and Computational Biology at the University of Maryland has released TopHat 1.4.0.

The latest release of TopHat includes new command-line options, enhancements in junction discovery for the segment-search method, and several bug fixes.


Genedata has released version 10 of Genedata Screener, its software for analyzing and managing plate-based data from high-content screening, high-throughput screening, and label-free and other time-series assays.

Included in this release are analytical capabilities such as dendrogram plots and full support for siRNA experiments. It supports multi-plate cell population analyses including capabilities for loading, aggregating, displaying, and storing millions of data points as well as interactive definition and display of cell populations by histograms among other improvements.


The European Bioinformatics Institute and Rothamsted Research have launched PhytoPath, a bioinformatics resource that integrates genome-scale data from important plant pathogen species with literature-curated information about the phenotypes of host infection.

The tool uses the Ensembl Genomes browser to provide access to complete genome assembly and gene models of agriculturally important fungal and oomycete plant pathogens. It links genes to experimentally verified functional information on disease progression in the host using data from the Pathogen Host Interactions database. PhytoPath also provides several analysis tools to help researchers compare predicted gene repertoires of pathogens with similar or dissimilar lifestyles.


St. Jude Children's Research Hospital and the Washington University School of Medicine have launched Explore, a freely available website that holds published research results from the Pediatric Cancer Genome Project, a research collaboration between the two institutions that aims to sequence the entire genomes of both normal and cancer cells from pediatric cancer patients.

According to the developers, the website provides access to high-quality genomic data related to pediatric cancers as well as comprehensive visualizations of the data. Users are provided with an overview of the genome project's progress; access to specific diseases; summaries of current discoveries; links to associated publications; views of single-patient genome data to disease levels; and other features.

The tool is designed to make it easier for clinical and basic researchers to search published results from the PCGP.


SoftGenetics has added a new stepwise paired end assembler for Illumina's MiSeq sequence data to its NextGENe software.

The new assembler resolves repeat region assembly problems and is best suited for assembling smaller genomes from short reads generated by Illumina's MiSeq platform.


PerkinElmer has launched Columbus 2.3, the latest version of its image data storage and analysis system.

This release features an improved version of PerkinElmer's machine-learning technology, PhenoLogic. It also includes changes to the user interface that make it similar to the instrument control software for PerkinElmer's Operetta High Content Imaging and Opera High Content Screening systems.


RefSeq Release 51 is now available from the National Center for Biotechnology Information via FTP.

This release incorporates genomic, transcript, and protein data available as of Jan. 10, and includes 19,580,946 records, 14,090,554 proteins, 2,908,099 RNAs, and sequences from 16,609 different organisms.


Filed under

The Scan

And For Adolescents

The US Food and Drug Administration has authorized the Pfizer-BioNTech SARS-CoV-2 vaccine for children between the ages of 12 and 15 years old.

Also of Concern to WHO

The Wall Street Journal reports that the World Health Organization has classified the SARS-CoV-2 variant B.1.617 as a "variant of concern."

Test for Them All

The New York Times reports on the development of combined tests for SARS-CoV-2 and other viruses like influenza.

PNAS Papers on Oral Microbiome Evolution, Snake Toxins, Transcription Factor Binding

In PNAS this week: evolution of oral microbiomes among hominids, comparative genomic analysis of snake toxins, and more.