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Gene Logic, GenePilot, GenBank, EMBL Nucleotide Sequence Database, BioBrew, BioJava 1.30, DictyBase

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Gene Logic has launched version 2.0 of its Genesis data integration, management, and analysis software for its GeneExpress database. Genesis 2.0 will be commercially available during the fourth quarter of 2003 to existing customers subscribed to the BioExpress System and/or the ToxExpress System, as part of their current subscription agreement.


GenePilot, a new microarray analysis software suite, is available from TG Services at www.genepilot.com. The suite includes hierarchical clustering, k-means clustering, self-organizing maps, and significance analysis of microarrays, as well as a Gene Ontology display in every result screen. GenePilot is free for academic users.


GenBank release 136.0 is now available from NCBI at ftp.ncbi.nih.gov. The release contains 32,528,249,295 base pairs and 25,592,865 entries, up by 1,428,984,840 base pairs and 1,564,929 sequence records from the April 135.0 release. Uncompressed, the 136.0 flat files require about 107 GB for the sequence files only. The ASN.1 version requires around 95 GB.


Release 75 of the EMBL Nucleotide Sequence Database is available from ftp://ftp.ebi.ac.uk/pub/databases/embl/release/ (UK), ftp://bio-mirror.net/biomirror/embl/release/ (US), and other mirror sites. Release 74 is about 17.2 GB compressed and 112 GB uncompressed and contains 25,214,767 sequences comprising 32,195,012,823 nucleotides, an increase of about 10 percent over release 74 in March.


Callident, a newly launched Linux cluster consulting company, will release BioBrew, an open source Linux cluster distribution based on the NPACI ROCKS software that is enhanced for bioinformaticists and life scientists, at ClusterWorld in San Jose, June 24-26. BioBrew includes all the software to build a cluster, along with the NCBI toolkit, Blast, mpiBlast, Hmmer, ClustalW, Gromacs, Wise, and EMBOSS.


BioJava 1.30 is available at http://www.biojava.org/download/. New features include packed storage of sequence data in memory, better support for the OBDA (open-bio database access) standards, and improvements to the parsers for output from Blast and Fasta. In addition, a BioJava tutorial/cookbook called “BioJava in Anger” is available at http://www.biojava.org/docs/bj_in_anger/index.htm.


An updated version of the DictyBase model organism database for Dictyostelium is available at http://dictybase.org.

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The Scan

Single-Cell Sequencing Points to Embryo Mosaicism

Mosaicism may affect preimplantation genetic tests for aneuploidy, a single-cell sequencing-based analysis of almost three dozen embryos in PLOS Genetics finds.

Rett Syndrome Mouse Model Study Points to RNA Editing Possibilities

Investigators targeted MECP2 in mutant mouse models of Rett syndrome, showing in PNAS that they could restore its expression and dial down symptoms.

Investigators Find Shared, Distinct Genetic Contributors to Childhood Hodgkin Lymphoma

An association study in JAMA Network Open uncovers risk variants within and beyond the human leukocyte antigen locus.

Transcriptomic, Epigenetic Study Appears to Explain Anti-Viral Effects of TB Vaccine

Researchers report in Science Advances on an interferon signature and long-term shifts in monocyte cell DNA methylation in Bacille Calmette-Guérin-vaccinated infant samples.