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Downloads and Upgrades : Feb 26, 2010


GenBank 176.0 is available via FTP from the National Center for Biotechnology Information. It contains data as of Feb. 19. The release contains approximately 112 billion base pairs and 116 million entries for non-WGS, non-CON sequences, and 163 billion base pairs and 57 million entries for WGS sequences.

Uncompressed, release 176.0 flatfiles require roughly 432 gigabytes for sequence only.

NCBI said that the average size of EST and GSS sequence files, uncompressed, has increased to about 500 MB with this release, compared to 222 MB in the previous release — a change that has reduced the total number of EST/GSS files by roughly 50 percent and "should make the FTP transfer of an entire release easier to manage, because the number of files is reduced, and their compressed sizes remain fairly small."

The Genome Browser team at the University of California at Santa Cruz has added a "gene" text box on the gateway and tracks pages of the UCSC Genome Browser.

Scientists searching for a particular gene without having the coordinates at the ready can enter the gene name into the text box and the software will offer gene names to choose from, UCSC said.

The European Bioinformatics Institute has announced the fourth release of Ensembl Genomes. This companion resource to Ensembl, the genome resources for vertebrates and other eukaryotes, provides access to genome-scale data for non-chordate species.

The release includes new databases for the bread mold Neurospora crassa, the slime mold Dictyostelium discoides, and the body louse Pediculus humanus.

The release also includes new variation databases for Drosophila melanogaster and Plasmodium falciparum; an update of the existing variation databases for Arabidopsis thaliana and Vitis vinifera; and the addition of three new clades to Ensembl Bacteria.

BioDiscovery has released Nexus DB, a repository that allows scientists to store, query, and share data arising from analyses with the firm's Nexus Copy Number software.

Nexus DB has been built using Amazon Elastic Compute Cloud with the data stored in Amazon Simple Storage Service, which has automated backup and built-in versioning control. It allows researchers to query "many datasets" at once and lets users specify individual and group level access and security features, BioDiscovery said.

SoftGenetics announced that its NextGene software now offers a merge function that lets users elongate reads, utilizing paired-end reads, to facilitate alignment, indel detection, and assembly.

The new functionality takes advantage of paired-end information, along with the additional coverage from sequenced overlapping DNA fragments, to produce long reads spanning the entire library size with an extremely low error rate, the company said.

Version 1.6.1 of the open source software suite Unipro Ugene is now available.

New features include a new aligner through integration of the KAlign algorithm, improved integration with the phylogenetic tool suite Phylip, and enhanced PhyTree and Alignment editors.

IDBS has released InforSense Suite 5.1, which helps scientists integrate, analyze, and visualize data. The new version lets users load their own data and customize the visualization tool charts in the software's VisualSense module.

The new version offers a portal search to help scientists retrieve and analyze their data. The platform also has "a new connector" for the R statistics package so users can directly access it from the software in order to analyze gene expression experimental results, for example.

LabVantage has launched Sapphire 5.1, the latest version of its laboratory information management suite. According to the firm, the software now offers "eForms," which can be configured according to a user's needs to capture clinical and patient data.

This new release also allows scientists to visualize data in real time via a grid and includes a spreadsheet-enabled interface. The platform also offers a management tool for clinical protocols and kits.

The Scan

Genome Sequences Reveal Range Mutations in Induced Pluripotent Stem Cells

Researchers in Nature Genetics detect somatic mutation variation across iPSCs generated from blood or skin fibroblast cell sources, along with selection for BCOR gene mutations.

Researchers Reprogram Plant Roots With Synthetic Genetic Circuit Strategy

Root gene expression was altered with the help of genetic circuits built around a series of synthetic transcriptional regulators in the Nicotiana benthamiana plant in a Science paper.

Infectious Disease Tracking Study Compares Genome Sequencing Approaches

Researchers in BMC Genomics see advantages for capture-based Illumina sequencing and amplicon-based sequencing on the Nanopore instrument, depending on the situation or samples available.

LINE-1 Linked to Premature Aging Conditions

Researchers report in Science Translational Medicine that the accumulation of LINE-1 RNA contributes to premature aging conditions and that symptoms can be improved by targeting them.