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Unipro DPview, GenBank, APS 3.0, JAligner, PerlPrimer, SVM RNAi 3.6, Pedro

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The UniPro Bioinformatics Group, a division of the Russian IT company UniPro, has released Unipro DPview, a software tool for visualizing and comparing genome sequences. DPview runs on Windows and is available for download at http://bits.unipro.ru/eng/dpview.html.


GenBank release 141.0 is now available from NCBI at ftp://ftp.ncbi.nih.gov/. The release contains 38,989,342,565 base pairs and 33,676,218 entries, up by 1,095,497,832 base pairs and 1,126,818 sequence records from the February 140.0 release. Uncompressed, the 141.0 flat files require about 131 GB for the sequence files only. The ASN.1 version requires around 115 GB.


Gepsoft has released a “pay as you go” version of its modeling software. The service allows users to create models using the demo version of its APS 3.0 software, and then extract the best model to a special file format. For a “small fee,” the company will unlock the encrypted version. The service is available at http://www.gepsoft.com/gepsoft/PayAsYouModel.htm.


JAligner, an open source Java implementation of the Smith-Waterman alignment algorithm, is available at http://jaligner.sourceforge.net.


Version 1.1.3 of PerlPrimer is available from Australia’s Murdoch Children’s Research Institute at http://perlprimer.sourceforge.net. The release includes several new primer design features, including the ability to design primers against a particular exon or range of exons, and the ability to design primers that do not overlap an intron/exon boundary.


SVM RNAi 3.6, a learning program for rational siRNA design, is available from Chang Bioscience at http://www.changbioscience.com/download/biotoolkit.html.


The University of Manchester has released Pedro at http://pedrodownload.man.ac.uk. Originally developed to support the Pedro (now MIAPE) proteomics data model, the program automatically renders data entry forms for a variety of XML schemas that can be used to create files that will validate against the original schema. Pedro can also load the MAGE genomics model.

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The Scan

Self-Reported Hearing Loss in Older Adults Begins Very Early in Life, Study Says

A JAMA Otolaryngology — Head & Neck Surgery study says polygenic risk scores associated with hearing loss in older adults is also associated with hearing decline in younger groups.

Genome-Wide Analysis Sheds Light on Genetics of ADHD

A genome-wide association study meta-analysis of attention-deficit hyperactivity disorder appearing in Nature Genetics links 76 genes to risk of having the disorder.

MicroRNA Cotargeting Linked to Lupus

A mouse-based study appearing in BMC Biology implicates two microRNAs with overlapping target sites in lupus.

Enzyme Involved in Lipid Metabolism Linked to Mutational Signatures

In Nature Genetics, a Wellcome Sanger Institute-led team found that APOBEC1 may contribute to the development of the SBS2 and SBS13 mutational signatures in the small intestine.