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EMBOSS, Urbigene, Ensembl 14, Dynamic Signaling Maps, SilicoCyte, ICM Browser

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EMBOSS Version 2.7.0 is available at http://www.uk.embnet.org/ Software/EMBOSS and ftp://ftp.uk.embnet.org/pub/EMBOSS. The new release includes improved sequence type handling, several bug fixes, and new programs, including Tcode, which tests DNA sequences for protein coding regions. In addition, the Jemboss GUI now includes a simple sequence alignment editor.

 

Urbigene, a molecular biology software package developed at Integragen, is now available under the GNU GPL at http://www.urbigene. com/PAGES/software.html. The software parses Blast results in XML format, and provides filters for Fasta sequences and Primer3 output, among other features.

 

Ensembl 14 is now available at www.ensembl.org. New features include version 2 of the zebrafish whole genome shotgun assembly, which has a total sequence length of 1.45 billion base pairs in 83,470 supercontigs. The mosquito SNP dataset has also been updated to dbSNP114.

 

Hippron Physiomics has released a new module for its Dynamic Signaling Maps pathway visualization software. The new module predicts biological signaling pathways and is freely available at http://www.hippron.com/hippron/index.html.

 

A free evaluation of the SilicoCyte microarray analysis software from CytoGenomics is available at http://www.silicocyte.com/int_dwnloads.htm. The software includes image analysis and data analysis features, as well as data management and data mining capabilities.

 

Molsoft has released a free bioinformatics, computational biology, and chemistry software tool called ICM Browser at http://www.molsoft.com/products/icm_browser.htm. The software reads PDB files, sequences, alignments or internal binary multi-object documents; contains sequence-structure visualization tools; provides a PDB search and visualization engine; calculates root mean square deviation between structures; and provides structure annotation.

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The Scan

Genetic Tests Lead to Potential Prognostic Variants in Dutch Children With Dilated Cardiomyopathy

Researchers in Circulation: Genomic and Precision Medicine found that the presence of pathogenic or likely pathogenic variants was linked to increased risk of death and poorer outcomes in children with pediatric dilated cardiomyopathy.

Fragile X Syndrome Mutations Found With Comprehensive Testing Method

Researchers in Clinical Chemistry found fragile X syndrome expansions and other FMR1 mutations with ties to the intellectual disability condition using a long-range PCR and long-read sequencing approach.

Team Presents Strategy for Speedy Species Detection in Metagenomic Sequence Data

A computational approach presented in PLOS Computational Biology produced fewer false-positive species identifications in simulated and authentic metagenomic sequences.

Genetic Risk Factors for Hypertension Can Help Identify Those at Risk for Cardiovascular Disease

Genetically predicted high blood pressure risk is also associated with increased cardiovascular disease risk, a new JAMA Cardiology study says.