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GenBank 168.0, Database — The Journal of Biological Databases and Curation, SRS version 8.3, ProteinCenter 2.0, SNP & Indel Viewer

GenBank 168.0 is available via FTP from the National Center for Biotechnology.
The new release contains 97,381,682,336 base pairs of non-whole-genome-shotgun sequence and 136,085,973,423 base pairs of WGS sequence. Uncompressed, the new release flatfiles require roughly 371 GB (sequence files only) or 396 GB, including the 'short directory', 'index' and the *.txt files.
The combined WGS/non-WGS single-release increase of 19.84 Gbp for release 168.0 is the largest that GenBank has experienced to date, GenBank curators said in an announcement.
GenBank 'index' files are now provided without any EST content, and without most GSS content. NCBI said it is considering ceasing support for the index files, and is encouraging users to review that section and provide feedback.
To distinguish what might be an approved or official gene symbol from its synonyms or alternatives, a new /gene_synonym qualifier has been introduced for GenBank Release 168.0. A new qualifier has been made available for non-sexual reproductive strategies.

Oxford University Press is accepting submissions for a new journal, Database — The Journal of Biological Databases and Curation.  
The idea behind the journal is to provide a platform for novel ideas in database research surrounding biological information. It aims “to help strengthen the bridge between database developers and users,” OUP said in an announcement.
The journal will publish detailed descriptions of databases and database tools, and authors “are strongly encouraged to include a biological discovery or a 'testable' hypothesis in their paper.” In addition, shorter papers describing significant updates to established databases will also run as well as reviews of complementary and ancillary databases and database tools alongside user tutorials and methodology and technical notes on database development.
More information is available here.

BioWisdom has announced the release of SRS version 8.3 to academics.
SRS 8.3 provides new functionality, an improved user interface, and support for the latest hardware and software platforms. It was released to commercial customers in January and has now been made available to academics at a “greatly reduced price,” the company said.
Improvements include a user annotation module and the ability to add protein and nucleic sequences to a personal database. SRS now supports RedHat AS/ES 4.0 in both 32-bit and 64-bit formats.

Proxeon has released ProteinCenter 2.0, a proteomics software tool that allows researchers to share datasets with colleagues and collaborators remotely and can “reveal the biological picture concealed within each dataset by enabling comparison of datasets against complete proteomes,” Proxeon said in a statement.
ProteinCenter is an annotated protein sequence database derived from all major protein databases to enable filtering, clustering, and statistical analysis from single, combined or comparison datasets, the company said.

SoftGenetics announced a new SNP & Indel viewer for its NextGene software suite for parallel sequencing systems. The company said the new tool permits gene annotation; navigation within the genome; view of variations in nucleotides and amino acids; links to the NCBI and dbSNP databases, and the ability to view and export consensus sequence.

Filed under

The Scan

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