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MTGD: The Medicago truncatula genome database.
Medicago truncatula, a close relative of alfalfa (Medicago sativa), is a model legume used for studying symbiotic nitrogen fixation, mycorrhizal interactions and legume genomics. J. Craig Venter Institute (JCVI; formerly TIGR) has been involved in M. truncatula genome sequencing and annotation since 2002 and has maintained a web-based resource providing data to the community for this entire period. The website (http://www.MedicagoGenome.org) has seen major updates in the past year, where it...
VIGOR extended to annotate genomes for additional 12 different viruses.
A gene prediction program, VIGOR (Viral Genome ORF Reader), was developed at J. Craig Venter Institute in 2010 and has been successfully performing gene calling in coronavirus, influenza, rhinovirus and rotavirus for projects at the Genome Sequencing Center for Infectious Diseases. VIGOR uses sequence similarity search against custom protein databases to identify protein coding regions, start and stop codons and other gene features. Ribonucleicacid editing and other features are accurately...
CharProtDB: a database of experimentally characterized protein annotations.
CharProtDB (/charprotdb/) is a curated database of biochemically characterized proteins. It provides a source of direct rather than transitive assignments of function, designed to support automated annotation pipelines. The initial data set in CharProtDB was collected through manual literature curation over the years by analysts at the J. Craig Venter Institute (JCVI) [formerly The Institute of Genomic Research (TIGR)] as part of their prokaryotic genome sequencing projects. The CharProtDB has...
The Protein Naming Utility: a rules database for protein nomenclature.
Generation of syntactically correct and unambiguous names for proteins is a challenging, yet vital task for functional annotation processes. Proteins are often named based on homology to known proteins, many of which have problematic names. To address the need to generate high-quality protein names, and capture our significant experience correcting protein names manually, we have developed the Protein Naming Utility (PNU, /pn-utility). The PNU is a web-based database for storing and applying...
Individual genomes instead of race for personalized medicine.
The cost of sequencing and genotyping is aggressively decreasing, enabling pervasive personalized genomic screening for drug reactions. Drug-metabolizing genes have been characterized sufficiently to enable practitioners to go beyond simplistic ethnic characterization and into the precisely targeted world of personal genomics. We examine six drug-metabolizing genes in J. Craig Venter and James Watson, two Caucasian men whose genomes were recently sequenced. Their genetic differences underscore...
Methanococcus jannaschii genome: revisited.
Analysis of genomic sequences is necessarily an ongoing process. Initial gene assignments tend (wisely) to be on the conservative side (Venter, 1996). The analysis of the genome then grows in an iterative fashion as additional data and more sophisticated algorithms are brought to bear on the data. The present report is an emendation of the original gene list of Methanococcus jannaschii (Bult et al., 1996). By using a somewhat more updated database and more relaxed (and operator-intensive)...
Whole-genome shotgun assembly and comparison of human genome assemblies.
We report a whole-genome shotgun assembly (called WGSA) of the human genome generated at Celera in 2001. The Celera-generated shotgun data set consisted of 27 million sequencing reads organized in pairs by virtue of end-sequencing 2-kbp, 10-kbp, and 50-kbp inserts from shotgun clone libraries. The quality-trimmed reads covered the genome 5.3 times, and the inserts from which pairs of reads were obtained covered the genome 39 times. With the nearly complete human DNA sequence [National Center...
Genome Solver Annotation Workshops
The Human Microbiome Project (HMP) has created a wealth of new questions for scientists. However, the current rate of microbial DNA sequencing far outpaces the ability of experts to analyze the genomes and metagenomes that have resulted from the HMP, creating a need for additional hands and minds to deal with the myriad of questions. This need in turn creates an opportunity for undergraduates to get involved in research on the HMP. Through the National Science Foundation (NSF) TUES...
J. Craig Venter Institute-led Team Awarded 5-year, $10.7 M Grant from U.S. Department of Energy to Optimize Metabolic Networks in Diatoms, Enabling Next-Generation Biofuels and Bioproducts
(LA JOLLA, CA)—October 3, 2017—Scientists, led by the J. Craig Venter Institute (JCVI), a not-for-profit genomic research organization, were recently awarded a 5-year, $10.7 million grant by the United States Department of Energy, Office of Science, Biological and Environmental Research (BER), BER Genomic Science Program to optimize metabolic networks in model photosynthetic microalgae, called diatoms. The aim of this work is to substantially increase oil, or lipid production, enabling...
Scientists from J. Craig Venter Institute and Scripps Institution of Oceanography Publish Study Describing Function and Mechanisms of Diatom Centromeres
(SAN DIEGO, CA)—July 6, 2017—A research team from the J. Craig Venter Institute (JCVI) and Scripps Institution of Oceanography at the University of California San Diego have published a paper today describing the DNA sequences from the centromeres of a type of microalgae, called diatoms. The research by first author Scripps Oceanography’s Rachel E. Diner, and senior author JCVI’s Philip D. Weyman, Ph.D., was published in the journal Proceedings from the National Academy of Sciences...