Ocimum Biosolutions has released Genowiz 4.0, a software package for gene expression analysis. New features include automated workflows for analyzing data, new organisms and genomes, automatic update of annotations, data export in different formats, box plots, and enhanced scatter plots.
GenBank 165.0 is available via FTP from the National Center for Biotechnology here.
The new release contains 89,172,350,468 base pairs of non-whole-genome-shotgun sequence and 110,500,961,400 base pairs of WGS sequence. Uncompressed, the 165.0 release flat files require about 332 GB for sequence files only. The ASN.1 data require approximately 305 GB.
The release includes a new GenBank division called Transcriptome Shotgun Assembly, or TSA. In addition, NCBI said that with the next release of GenBank, scheduled for June, it will no longer provide a single, comprehensive protein FASTA file for GenBank releases.
NCBI has also activated a new URL for Blast searches: http://blast.ncbi.nlm.nih.gov.
NCBI said that searches sent to this URL “can take advantage of a larger number of machines” and recommended migrating all Blast links and bookmarks to the new URL.
The University of California, Santa Cruz, Genome Bioinformatics Group has released the Archaeal Genome Browser Database, a visualization tool and integrated repository for archaeal functional genomics data. The database, developed by Todd Lowe’s group in the UCSC Biomolecular Engineering Department, includes information on more than 50 completed archaeal genomes.
UCSC has also released a Genome Browser and Blat server for the Callithrix jacchus marmoset genome, which was produced by Washington University St. Louis School of Medicine Genome Sequencing Center.
The C. jacchus genome was sequenced to 6X coverage using DNA from a female marmoset provided by the Southwestern National Primate Research Center in San Antonio, TX. The assembly is composed of 49,724 supercontigs containing a total of around 3.02 billion bases.
Downloads of sequence and annotations are available from the Genome Browser FTP server or Downloads page.