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Downloads and Upgrades: Jul 8, 2011

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BGI has released updated versions of its Short Oligonucleotide Analysis Package, including SOAP3 GPU/CPU, SOAPdenovo 2, SOAPindel, and SOAPsv.

Simultaneously, BGI also launched two new cloud-based distributed solutions, Hecate and Gaea, for de novo assembly and genome resequencing.


GenBank 184.0 is now available via FTP from the National Center for Biotechnology Information.

Uncompressed 184.0 flatfiles require roughly 506 gigabytes for sequence files only or 543 gigabytes to include the short directory, index, and text files. The ASN.1 data require approximately 416 gigabytes.


Ensembl 63 is available here.

The release includes a new high-coverage assembly for microbat, Myotis lucifugus, the most recent human and zebrafish manual gene annotations from HAVANA, and updated mouse variation data.


Agilent has released a new version of CytoGenomics, the firm's comparative genomic hybridization and CGH+SNP microarray data analysis and reporting solution.

Version 1.5 lets users compare in-house data to external databases such as the Online Mendelian Inheritance in Man database; automate TIFF image upload, feature extraction, and analysis; and generate custom reports among other features.


This week, Geschickten announced a beta release of iOmics, its cloud-based solution for next-generation sequence data analysis.

The platform includes tools to identify novel genes associated with rare and common disorders, identify protein binding sites and novel transcripts, perform comparative analysis, and identify target genes of discovered miRNAs. It also includes tools for single nucleotide variation and copy number variation detection.

Interested researchers are invited to sign up for a seven-day trial. The company plans to release additional version of the platform later this year (BI 06/03/2011).


Genedata has launched Genedata Biologics 1.5, the latest version of its enterprise solution for biologics research and development.

The newest version of the tool supports cross-departmental and external data exchange as well as technology transfer among research partners, such as pharmaceutical and biotech companies, technology providers, contract research organizations, and academic research networks.


The Scan

Breast Cancer Risk Related to Pathogenic BRCA1 Mutation May Be Modified by Repeats

Several variable number tandem repeats appear to impact breast cancer risk and age at diagnosis in almost 350 individuals carrying a risky Ashkenazi Jewish BRCA1 founder mutation.

Study Explores Animated Digital Message Approach to Communicate Genetic Test Results to Family Members

In the Journal of Genetic Counseling, the approach showed promise in participants presented with a hypothetical scenario related to a familial hereditary breast and ovarian cancer syndrome diagnosis.

Computational Tool Predicts Mammalian Messenger RNA Degradation Rates

A tool called Saluki, trained with mouse and human messenger RNA data, appears to improve mRNA half-life predictions by taking RNA and genetic features into account, a Genome Biology paper reports.

UK Pilot Study Suggests Digital Pathway May Expand BRCA Testing in Breast Cancer

A randomized pilot study in the Journal of Medical Genetics points to similar outcomes for breast cancer patients receiving germline BRCA testing through fully digital or partially digital testing pathways.