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Downloads and Upgrades: Velvet Optimiser 2.2.4; MacVector 12.6; Ensembl 68; and more


Researchers from the Victorian Bioinformatics Consortium have released version 2.2.4 of the Velvet Optimiser, which includes a several bug fixes.

MacVector has released version 12.6 of its software, which provides tools for sequence editing, primer design, internet database searching, protein analysis, sequence confirmation, multiple sequence alignment, phylogenetic reconstruction, coding region analysis, and other functions.

MacVector 12.6 includes a new interactive tool for designing primers, dubbed QuickTest Primer, and lets users import annotation from genome browsers with support of GFF, GFF3, and BED files to annotate blank sequences. The developers have also improved the tool’s ability to display large assemblies and import existing BAM/SAM and ACE alignments for display among other updates

Ensembl release 68 is available here.

The release includes updates to the human assembly and the human somatic variants from the Catalogue of Somatic Mutations in Cancer. It also includes a new species, Chinese softshell turtle (Pelodiscus sinensis) and updated assemblies for mouse and dog.

Certara subsidiary Simcyp has released version 12 of its Population-based Simulator, a platform for quantitative prediction of drug-drug interactions and pharmacokinetic-pharmacodynamic outcomes in both healthy subjects and diverse patient populations.

The release includes an implementation of a mechanistic kidney model, expanded drug distribution models, and enhancements and additions to its compound libraries and pediatric module. It also incorporates physiologically based pharmacokinetic models for therapeutic proteins which can be use in the development of biologics.

The Protein Data Bank has released two tools to help users prepare data files for deposition with its AutoDep Input Tool or ADIT.

pdb_extract is an online tool which assembles details about experiments and experimental models from coordinate and structure determination output files in preparation for PDB deposition. It extracts key details from the output files produced by X-ray crystallographic and NMR applications. It then merges these data into mmCIF data files that can be used with ADIT for validation and deposition.

SF-Tool is a web-based tool for validating X-ray, neutron, and hybrid experimental data. It validates model coordinates against structure factor data; convert structure factor files between different formats; and check for and validate twinned or detwinned data among other capabilities.