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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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