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Blast 2.2.16, GeneDirector 3.5, UCSC Genes, Image-Pro Plus Version 6.2, Merlin version 1.1

The National Center for Biotechnology Information has released Blast 2.2.16 here. The new release includes performance improvements for nucleotide searches and some bug fixes. This will be the last release for Solaris 8 and Tru64, NCBI said. 

BioDiscovery has released GeneDirector 3.5. The new version of the software includes “extended” data management support for Affymetrix, Illumina, and Agilent microarray platforms, the company said. GeneDirector 3.5 includes several “major upgrades” to its backend data-management engine in order to improve support for these microarray platforms, the company said.

The Genome Bioinformatics Group at the University of California, Santa Cruz, has released a new gene prediction set, UCSC Genes, via the UCSC Genome Browser (hg18, NCBI Build 36). The annotation set includes putative non-coding genes as well as protein-coding genes and 99.9 percent of RefSeq genes. It supersedes the existing Known Genes annotation on the hg18 assembly, UCSC said.
In conjunction with the release of the UCSC Genes data set, UCSC has also released companion annotation track on the hg18 assembly called Alt Events, which shows alternative splicing, alternative promoter, and other events that result in more than a single transcript from the same gene.

Media Cybernetics has released Image-Pro Plus Version 6.2. The new version of the company’s scientific image processing and analysis software includes the ability to remove haze from image stacks via built-in SharpStack image deconvolution tools. These tools include real-time 2D deconvolution, nearest neighbor and no-neighbor deconvolution, and the inverse filter algorithm.

An alpha release of Merlin version 1.1 is available here. The release includes support for estimation of missing genotypes and support for quantitative trait association analyses. There are also several other smaller enhancements, including support for base-pair allele labels in pedigree files.

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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.