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OpGen, microArrayDB 1.0, Threader, zEST, EMBL, InterPro 7.1, Treefinder, AMIGO

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Single-molecule DNA analysis firm OpGen has completed a whole-genome map of the infectious bacterium Francisella tularensis — the first in a series of such maps that the company is generating for Category A bio-threat agents.


Array Genetics has released microArrayDB 1.0, a web-based DNA microarray project- and data-management system. Researchers can use the software to enter DNA microarray project information, including details of each cRNA target as well as Affymetrix GeneChip specifications, via a web browser. All information is recorded using a MySQL database on the client’s server, and the software enables users to share microarray data with others via the web interface.


Version 3.4 of the Threader protein fold recognition software is available from the bioinformatics unit at University College London at http://bioinf.cs.ucl.ac.uk/threader/. The upgrade includes an experimental Web utility to allow additional structures to be added to the standard fold library.


UCL’s bioinformatics unit has also released transcriptome data for Apis mellifera (honey bee), Takifugu rubripes (fugu), Schistosoma mansoni (bilharziose worm), and Anopheles gambiae (mosquito) at http://bioinformatics.org/zEST. The data was derived by processing publicly available EST and mRNA sequences with the zEST transcriptome assembly software.


Release 77 of the EMBL Nucleotide Sequence Database is available from ftp://ftp.ebi.ac.uk/pub/databases/embl/release/ (UK), ftp://biomirror.net/biomirror/embl/release/ (US), and other mirror sites. Release 77 is about 19 GB compressed and 129 GB uncompressed and contains 30,351,263 sequences comprising 36,042,464,651 nucleotides, an increase of about 5 percent over release 76 in September.


InterPro 7.1 is available from the European Bioinformatics Institute at http://www.ebi.ac.uk/interpro/. The database, an integrated resource combining protein families, domains, and functional sites from Swiss-Prot, Trembl, Prosite, Prints, Pfam, and ProDom, now contains 10,403 entries, representing 2,239 domains, 7,901 families, 197 repeats, 26 active sites, 20 binding sites and 20 post-translational modifications.


A new version of the Treefinder software for calculating phylogentic trees is available at www.treefinder.de. New features include a utility for computing rate profiles along sequence alignments, and calibration of phylogenetic trees via a nonparametric rate smoothing method.


The USDA-ARS Livestock Issues Research Unit has released a new graphical front end for AMIGO and GO at http://199.133.147.101/cgi-bin/species/index.pl.

 

Filed under

The Scan

Study Tracks Responses in Patients Pursuing Polygenic Risk Score Profiling

Using interviews, researchers in the European Journal of Human Genetics qualitatively assess individuals' motivations for, and experiences with, direct-to-consumer polygenic risk score testing.

EHR Quality Improvement Study Detects Demographic-Related Deficiencies in Cancer Family History Data

In a retrospective analysis in JAMA Network Open, researchers find that sex, ethnicity, language, and other features coincide with the quality of cancer family history information in a patient's record.

Inflammatory Bowel Disease Linked to Gut Microbiome Community Structure Gradient in Meta-Analysis

Bringing together data from prior studies, researchers in Genome Biology track down microbial taxa and a population structure gradient with ties to ulcerative colitis or Crohn's disease.

Ancient Greek Army Ancestry Highlights Mercenary Role in Historical Migrations

By profiling genomic patterns in 5th century samples from in and around Himera, researchers saw diverse ancestry in Greek army representatives in the region, as they report in PNAS.