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Downloads and Upgrades: BLAST databases, GenBank 198.0, Bina's RNA-seq Data Analysis, and more


The National Center for Biotechnology Information has updated its organism BLAST databases to use top-level — chromosome + unplaced and unlocalized scaffolds — RefSeq genomic records instead of scaffold records. This change has also been made for the human and mouse G+T BLAST databases.

NCBI has also released GenBank 198.0 via ftp.

Uncompressed 190.0 flatfiles require roughly 613 gigabytes for sequence files only. The ASN.1 data require approximately 504 gigabytes.

Bina Technologies has added RNA-sequence data analysis capabilities to its genomic analysis platform.

The RNA-Seq workflow includes open-source software tools such as TopHat2, Bowtie2, and Cufflinks. It also supports multiple sample merging, a feature than enhances transcript identification. According to the company, customers can use the platform to process up to 1,000 RNA-Seq samples per month.

ChemAxon has released JChem for Office, a unified series of chemistry functionality that is available directly within the Microsoft Office suite.

Features include the ability to embed live chemical structures from existing files, support for all major common chemistry file types, and the ability to sketch and edit structures on the fly. Other features include changes to the JChem for Excel product which now has tools for working with R-Group decomposition, complex queries, corporate ID’s and SAR table generation.

Version 3.0.2 of BiNGO, a tool that's used to determine which Gene Ontology categories are statistically overrepresented in gene sets or biological networks, is now available from the Cytoscape app store.

The release includes fixes to execution-order issues that could potentially cause incorrect results, and repairs to the batch processing mode and the ability to analyze networks containing mixed-case or lowercase gene identifiers.

BioBase has launched the PharmacoGenomic Mutation Database, or PGMD, a new database of detailed genotype-phenotype relationships derived from in vivo pharmacogenomic patient studies. The information in the resources comes mostly from clinical trials and provides insights into things like response rate, risk of adverse events, realization of expected outcomes pharmacokinetic parameters such as dose requirements, and much more.

The genome browser group at the University of California, Santa Cruz has released four tracks for the human genome assembly, that are derived from dbSNP build 138.

The new tracks contain additional annotation data not included in previous dbSNP tracks, with corresponding coloring and filtering options in the genome browser.

OpenEye Scientific Software has released OpenEye Toolkits v2013.Oct.

Languages supported in this release include C++, Python, .NET, and Java. Features include repackaged Python toolkits, improvements to the 'ROCS report' feature, and a significant bug fix for Java on Linux.

Cartagenia has released a new version of its Bench Lab NGS software, a tool for NGS variant analysis, interpretation, and reporting pipelines.

This version includes flexible templates that labs can adapt; and it introduces a nuclear family analyses that takes into account parent and sibling genotype and affected status, as well as the mode of inheritance hypotheses. It also includes updated version tracking, validated target panels, and controlled transition to new annotation sources, among other updates.