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Araport: the Arabidopsis information portal.
The Arabidopsis Information Portal (https://www.araport.org) is a new online resource for plant biology research. It houses the Arabidopsis thaliana genome sequence and associated annotation. It was conceived as a framework that allows the research community to develop and release 'modules' that integrate, analyze and visualize Arabidopsis data that may reside at remote sites. The current implementation provides an indexed database of core genomic information. These data are made available...
The genetic map and comparative analysis with the physical map of Trypanosoma brucei.
Trypanosoma brucei is the causative agent of African sleeping sickness in humans and contributes to the debilitating disease 'Nagana' in cattle. To date we know little about the genes that determine drug resistance, host specificity, pathogenesis and virulence in these parasites. The availability of the complete genome sequence and the ability of the parasite to undergo genetic exchange have allowed genetic investigations into this parasite and here we report the first genetic map of...
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species.
AmoebaDB (http://AmoebaDB.org) and MicrosporidiaDB (http://MicrosporidiaDB.org) are new functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. The databases belong to the National Institute of...
UC San Diego Partners with Venter Institute to Build Community Cyberinfrastructure for Advanced Marine Microbial Ecology Research and Analysis
January 17, 2006 — Researchers at the University of California, San Diego (UCSD) will build a state-of-the-art computational resource and develop software tools to decipher the genetic code of communities of microbial life in the world's oceans. The new resource will help scientists understand how microbes function in their natural ecosystems, enable studies on the effect humans are having on the environment, as well as permit insight into the evolution of life on Earth. The UCSD...
TIGRFAMs and Genome Properties: tools for the assignment of molecular function and biological process in prokaryotic genomes.
TIGRFAMs is a collection of protein family definitions built to aid in high-throughput annotation of specific protein functions. Each family is based on a hidden Markov model (HMM), where both cutoff scores and membership in the seed alignment are chosen so that the HMMs can classify numerous proteins according to their specific molecular functions. Most TIGRFAMs models describe 'equivalog' families, where both orthology and lateral gene transfer may be part of the evolutionary history, but...
Multilocus sequence typing system for the endosymbiont Wolbachia pipientis.
The eubacterial genus Wolbachia comprises one of the most abundant groups of obligate intracellular bacteria, and it has a host range that spans the phyla Arthropoda and Nematoda. Here we developed a multilocus sequence typing (MLST) scheme as a universal genotyping tool for Wolbachia. Internal fragments of five ubiquitous genes (gatB, coxA, hcpA, fbpA, and ftsZ) were chosen, and primers that amplified across the major Wolbachia supergroups found in arthropods, as well as other divergent...
Analysis of the transcriptome of the protozoan Theileria parva using MPSS reveals that the majority of genes are transcriptionally active in the schizont stage.
Massively parallel signature sequencing (MPSS) was used to analyze the transcriptome of the intracellular protozoan Theileria parva. In total 1,095,000, 20 bp sequences representing 4371 different signatures were generated from T.parva schizonts. Reproducible signatures were identified within 73% of potentially detectable predicted genes and 83% had signatures in at least one MPSS cycle. A predicted leader peptide was detected on 405 expressed genes. The quantitative range of signatures was...
Composite genome map and recombination parameters derived from three archetypal lineages of Toxoplasma gondii.
Toxoplasma gondii is a highly successful protozoan parasite in the phylum Apicomplexa, which contains numerous animal and human pathogens. T.gondii is amenable to cellular, biochemical, molecular and genetic studies, making it a model for the biology of this important group of parasites. To facilitate forward genetic analysis, we have developed a high-resolution genetic linkage map for T.gondii. The genetic map was used to assemble the scaffolds from a 10X shotgun whole genome sequence,...
New Pathogen Discovery in Travelers’ Diarrhea by Metagenomic Sequencing
Diarrheal disease affects one billion people per year worldwide, yet >80% of these cases are of unknown etiology. Travelers’ diarrhea or TD, affects between 20 to 60% of those who travel from developed to low-income countries and impacts 20-40 million travelers worldwide each year. Bouts of travelers’ diarrhea can predispose to development of post-infectious irritable bowel disease (IBD). The travelers are often immunologically naïve to the pathogens that they encounter in the...
Richard H. Scheuermann, Ph.D. Joins J. Craig Venter Institute as Director of Informatics
SAN DIEGO, CA and ROCKVILLE, MD — April 12, 2012 — The J. Craig Venter Institute (JCVI) today announced that Richard H. Scheuermann, Ph.D. has joined the organization as the Director of Informatics effective May 1, 2012. He will be based in the San Diego, California facility and is responsible for leading and directing the informatics programs at both the JCVI Rockville, Maryland and San Diego campuses. "We are very pleased to have Richard as part of the JCVI team," said J....