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MDL Information Systems, GenomeExplorer, Baylor College of Medicine Rat Genome Sequencing Center, Dalke Scientific Software, Nucleic Acids Research

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MDL Information Systems has released MDL Core Interface 1.0, the middleware server for its three-tier application development architecture, MDL Discovery Framework. MDL Core Interface can be used to integrate MDL and non-MDL applications and databases, and provides access to Java application programming interfaces for custom software development. It also provides an integrating foundation for all of MDL’s new products, including the company’s DiscoveryGate web-based research environment.

Draft genome annotation for rat from Softberry’s Fgenesh++ gene prediction software is available from Softberry’s GenomeExplorer at: www.softberry.com/berry.phtml? topic=ratexp, as well as the University of California, Santa Cruz, genome browser at: http://genome.ucsc.edu/cgi-bin/hgGateway?org=Rat. The annotation, which used the Nov. 2002 rat assembly produced by the Baylor College of Medicine Rat Genome Sequencing Center and the Rat Genome Sequencing Consortium, contains 43,008 genes, including 28,955 genes supported by non-redundant proteins, and 3,763 genes corresponding to rat Refseq mRNA.

Dalke Scientific Software has released EUtils 1.0, a Python library for the Entrez databases at NCBI, at: www.dalkescientific.com/EUtils/. The package allows developers to write programs that directly query the NCBI databases via Entrez.

The annual Nucleic Acids Research database issue is available at http://nar.oupjournals.org/content/vol31/issue1/. The issue, which includes papers on 129 biological databases, is freely available online to subscribers and non-subscribers of the journal.

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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.