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BatchMatch, RAMP, TopBioMarkers, Primer-Blast, GeneMarker, Ensembl 50. UCSC Genome Browser

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Systems Analytics has launched three software products: BatchMatch, RAMP, and TopBioMarkers.
 
BatchMatch is designed for quantifying and removing batch effects in microarray data. The software evaluates and removes batch effects, facilitates the integrated study of multiple datasets, and enhances the statistical confidence in the detection of reproducible biological signals, the company said.
 
RAMP, or Robust Accurate Modeling Protocol, is designed for constructing predictive models using expression data. It includes an automatic workflow to generate and select high-performance predictive models “that are reliable, robust, reproducible and generalizable to new datasets,” the company said.
 
TopBioMarkers is designed for identifying potential markers with strong predictive power and high reproducibility from expression data with multiple classes, such as dose groups and time points.
 

 
The National Center for Biotechnology Information has released Primer-Blast, a tool that combines primer design using Primer3 with a specificity check using Blast.
 
NCBI said that Primer-BLAST was developed to help users make primers that are specific to a PCR template. The specificity check against user-selected databases “can avoid primer pairs that amplify targets other than the input template,” NCBI said.
 

 
SoftGenetics has released an update for its GeneMarker genotyping software. GeneMarker 1.75 offers SNP analysis using the TILLING (Targeting Induced Local Lesions in Genomes) technique on capillary electrophoresis data.
 
GeneMarker 1.75 also includes an enhanced Human Identification Module for use in paternity and other STR-based human identification analysis. The software also includes other new features, such as the ability to view multiple analysis projects to speed reviewing and editing of AFLP and other investigations; the ability to display Euclidian
distance in dendograms with a mouse-over; and a new file name group editor.
 

 
Ensembl 50 is available here.
 
The new release includes the latest Bos taurus assembly, Btau_4.0, and a corresponding new genebuild, as well as a new C. elegans release, a new genebuild for Ochotona princeps, and an updated genebuild for Felis catus.
 
Ensembl Human includes a new gene set, and an improved merge between Ensembl-predicted genes and the latest Havana manually-annotated gene set.
 
The Ensembl development team said it is also working on a new website design that it expects to be ready for testing in August. Those interested in testing the new site should submit their e-mail address to [email protected].
 

 
The University of California, Santa Cruz, Genome Bioinformatics Group has released a Genome Browser for the latest C.  elegans assembly, based on sequence version WS190 deposited into WormBase in May.
 
Bulk downloads of the sequence and annotation data are available via the UCSC Genome Browser FTP server or downloads page.

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