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Pedant-Pro Sequence Analysis Suite, ToxFX Analysis Suite, GeneChip Rat ToxFX 1.0 Array, Rat Genome 230 2.0 Array, MIFit 3.1, RefSeq 20


Biomax Informatics has released version 3 of its Pedant-Pro Sequence Analysis Suite for automatically annotating individual sequences and complete genomes. The new release includes a new workflow architecture and a new user interface. The software is available as an in-house solution or as hosted service at the Biomax website.

Affymetrix and Iconix Biosciences have jointly launched the ToxFX Analysis Suite, a toxicogenomics analysis system that combines Iconix’ automated analysis with Affy GeneChips to generate a compound safety profile. ToxFX users first generate gene-expression data from rat samples on either the GeneChip Rat ToxFX 1.0 Array or the Rat Genome 230 2.0 Array. The data are then compared to the Iconix Drug Signatures and pathway response libraries and cross-referenced to identify matches to known toxicological responses in order to generate a toxicity profile for the compound. Affymetrix is marketing the ToxFX Analysis Suite, which includes ToxFX 1.0 GeneChip microarrays with “Analysis Certificates.” An individual Analysis Certificate, which enables data from a single array to be compared with the reference database, can be purchased directly from Iconix.

MIFit 3.1, a crystallographic model-building program, is available from Molecular Images here New features include a full refinement interface for use with CCP4 and REFMAC5, as well as a display of crystal cell axes, more efficient generation of symmetry related atoms, a “sequence view” that follows the active model, distance labels on H-bond displays, and graphical display of distance monitors.

RefSeq 20 is available here from the National Center for Biotechnology Information. RefSeq 20 includes 4,567,569 records, 3,000,705 proteins, and sequences from 3,919 different organisms.

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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.