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Downloads and Upgrades: Oct 21, 2011

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Appistry has released a series of RNA-seq data analysis tools for Ayrris/Bio, a cloud platform for next-generation sequence data analysis that the company launched in September (BI 9/9/2011).

These new tools, which are based on TopHat, TopHat-Fusion, and MapSplice, support alignment, transcript assembly, splice variant prediction, and expression level determination. They also provide algorithms for calling SNPs, rare variants, and insertions and deletions.


The National Center for Biotechnology Information has released GenBank 186.0 via ftp.

Uncompressed186.0 flatfiles require roughly 518 gigabytes for sequence files only or 557 gigabytes to include the short directory, index, and text files. The ASN.1 data requires approximately 426 gigabytes.

NCBI has also launched dbSNP Build 135 for the human genome.

The complete data for build 135 can be found here.

The complete build summary for 135 is available here.

This release is based on NCBI genome build GRCh37.3 and includes assembly changes and new submissions from the 1000 Genomes Project phase I release


The ENCODE Data Coordination Center at the University of California, Santa Cruz, has released a new histone modifications track and corrected previously released RNA-binding protein datasets.


Researchers at the laboratory for optical and computational instrumentation at the University of Wisconsin, Madison, and Glencoe Software have released Bio-Formats 4.3.3.

The release fixes several bugs from previous versions.


MetaVelvet 1.1.01 is now available.

This release includes several bug fixes and modifications to the graph split algorithm


The second version of the Database of Genomic Variants was launched this week.

DGV – also known as “the Toronto Database” – is a public repository that houses human genomic copy number and structural variants. It was created in 2004 by researchers at the Center for Applied Genomics, the Hospital for Sick Children, and the University of Toronto’s McLaughlin Center.

This release expands on DGV's previous content to include new genomic variants as well as interactive query tools and interfaces for viewing complex data originating from genome scanning experiments.


The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.