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Genome Properties
The Genome Properties system consists of a suite of "Properties" which are carefully defined attributes of prokaryotic organisms whose status can be described by numerical values or controlled vocabulary terms for individual completely sequenced genomes. The Genome Properties database, specifies how computed evidence, including TIGRFAMs HMM results, should be used to judge whether an enzymatic pathway, a protein complex or another type of molecular subsystem is encoded in a genome. TIGRFAMs and...
TIGRFAMS
TIGRFAMs is a database of protein family definitions. Each entry features a seed alignment of trusted representative sequences, a hidden Markov model (HMM) built from that alignment, cutoff scores that let automated annotation pipelines decide which proteins are members, and annotations for transfer onto member proteins. Most TIGRFAMs models are designated equivalog, meaning they assign a specific name to proteins conserved in function from a common ancestral sequence. Models describing more...
Identification of Misclassified ClinVar Variants via Disease Population Prevalence.
There is a significant interest in the standardized classification of human genetic variants. We used whole-genome sequence data from 10,495 unrelated individuals to contrast population frequency of pathogenic variants to the expected population prevalence of the disease. Analyses included the ACMG-recommended 59 gene-condition sets for incidental findings and 463 genes associated with 265 OrphaNet conditions. A total of 25,505 variants were used to identify patterns of inflation (i.e., excess...
Elvira
The name Elvira stands for Executive for Large-scale VIRal Assembly. Elvira is a collection of tools and scripts used at JCVI for sequence and metadata tracking, sequence assembly, coverage and other analysis, and generation of reports. The majority of the code is written in Java (ElviraJava), with several Perl and PHP scripts and libraries. Elvira was developed at TIGR (now JCVI) where it contributed to the sequencing and publication of thousands of viral genomes. This software...
VIGOR
VIGOR (VIral Genome ORF Reader) is a homology-driven viral gene finder capable of predicting proteins, polyproteins and mature peptides. VIGOR is able to identify and properly handle typical viral transcriptional and translational exceptions, like ribosomal slippage, RNA editing, stop codon readthrough, etc. The package consists of the software and a collection of highly-curated reference databases, one for each type of virus VIGOR is capable to annotate. Enabling VIGOR to annotate a new...
Resolving the Bottleneck in Antibiotic Discovery
The goal of this multicomponent project is to develop an efficient transcriptomic approach to dereplicate antibacterial extracts of pure isolates of uncultured soil bacteria, revealing which are chemically identical to known antibiotics. Leveraging our expertise in transcriptomics at JCVI and in collaboration with Dr. Kim Lewis (Northeastern University) and Dr. Amy Spoering (NovoBiotic), we will develop an effective discovery program based on exploiting uncultured bacteria to resolve the...
Optimizing Phagehunting Methods to Isolate and Amplify Bacteriophages
Shriya Singh, Enrique Assad-Garcia, Nacyra Assad-Garcia, Lauren Oldfield, Sanjay Vashee, and Derrick E. Fouts J. Craig Venter Institute, Rockville, MD 20872 There are an estimated 1031 bacteriophages (phage), viruses that infect bacteria, in the biosphere, thus comprising a significant portion of the biosphere on Earth. Of these, a mere 10,733 phages have been isolated and 2,061 phages have sequenced, complete genomes, with even fewer, only 1,073,...
Advanced Bioinformatics Workshop, International Livestock Research Institute, Nairobi, Kenya
Advanced bioinformatics workshop was conducted at International Livestock Research Institute, Nairobi, Kenya. Day 1: Basics of Bioinformatics Mark Wamalwa, Joyce Njuguna, Dedan Githae, Nelson Ndegwa, Koko Mutai Introduction to Linux Hands on command line LINUX Day 2: Bioinformatics Resources for data management. Mark...
The DBCLS BioHackathon: standardization and interoperability for bioinformatics web services and workflows. The DBCLS BioHackathon Consortium*.
Web services have become a key technology for bioinformatics, since life science databases are globally decentralized and the exponential increase in the amount of available data demands for efficient systems without the need to transfer entire databases for every step of an analysis. However, various incompatibilities among database resources and analysis services make it difficult to connect and integrate these into interoperable workflows. To resolve this situation, we invited domain...
GreenPhylDB v2.0: comparative and functional genomics in plants.
GreenPhylDB is a database designed for comparative and functional genomics based on complete genomes. Version 2 now contains sixteen full genomes of members of the plantae kingdom, ranging from algae to angiosperms, automatically clustered into gene families. Gene families are manually annotated and then analyzed phylogenetically in order to elucidate orthologous and paralogous relationships. The database offers various lists of gene families including plant, phylum and species specific gene...