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Downloads and Upgrades: Sequencher 5.2, Syapse, CytoSure Interpret 4.5.3, and more


Gene Codes has released Sequencher 5.2, the latest version of its DNA sequence data analysis software. The release includes a new application called Sequencher Connections that, among other capabilities, lets users integrate the software with third party tools; and run Blast searches in multiple databases simultaneously and then compare the results. Other updates include the addition of the BWA algorithm and expanded licensing options for the software.

Syapse said this week that it will allow third-party commercial omics interpretation providers to make their content available to Syapse customers through its platform. It will release the names of supported third-party providers in the coming weeks. The company also said that customers will be able to integrate public and open databases, such as ClinVar, COSMIC, PhenoDB, and OMIM, through standard connectors in its platform.

The Worldwide Protein Data Bank said this week that it has made validation reports for all X-ray crystal structures in the PDB archive publicly available. These reports implement the recommendations of a large group of community experts on validation and include the results of geometric checks, structure-factor assessment. and ligand validation. They also include results from software such as MolProbity, Xtriage, Mogul, EDS, as well as various CCP4 programs.

Oxford Gene Technology has released version 4.5.3 of its CytoSure Interpret software, an analysis package for aCGH data. The release includes features such as automatic aberration classification and gives users the choice to run a standardized data analysis pipeline or customize it for their purposes.

Cufflinks 2.2.0 is available here.

Features included in this release include two new programs — cuffquant and cuffnorm — that make it easier to quantify gene expression in experiments with many samples. This version also offers sample sheets and contrast files which also make it easier to work with large-scale analyses.

Elsevier has launched the QUOSA for iPad application in order to provide customers with mobile access to copyright compliant literature. According to the company, the resource will enable medical affairs teams and medical science liaisons remote access to pre-approved and copyright compliant literature, which can be read offline, from a central repository. This includes articles from sources such as PubMed and Embase.

Researchers involved in the Functional Annotation of the Mammalian Genome (FANTOM) project have released a comprehensive map of the way genes work across the major cells and tissues of the human body. The map describes the complex networks that govern gene activity and could play a crucial role in identifying the genes involved with disease, according to the developers.

The study is the result of a years-long collaborative effort among 250 experts from more than 20 countries. The FANTOM project, led by the Japanese institution RIKEN, aims to build a complete library of human genes.

The Scan

Purnell Choppin Dies

Purnell Choppin, a virologist who led the Howard Hughes Medical Institute, has died at 91, according to the Washington Post.

Effectiveness May Decline, Data From Israel Suggests

The New York Times reports that new Israeli data suggests a decline in Pfizer-BioNTech SARS-CoV-2 vaccine effectiveness against Delta variant infection, though protection against severe disease remains high.

To See Future Risk

Slate looks into the use of polygenic risk scores in embryo screening.

PLOS Papers on Methicillin-Resistant Staphylococcus, Bone Marrow Smear Sequencing, More

In PLOS this week: genomic analysis of methicillin-resistant Staphylococcus pseudintermedius, archived bone marrow sequencing, and more.