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InterPro in 2019: improving coverage, classification and access to protein sequence annotations.
The InterPro database (http://www.ebi.ac.uk/interpro/) classifies protein sequences into families and predicts the presence of functionally important domains and sites. Here, we report recent developments with InterPro (version 70.0) and its associated software, including an 18% growth in the size of the database in terms on new InterPro entries, updates to content, the inclusion of an additional entry type, refined modelling of discontinuous domains, and the development of a new programmatic...
Fighting Back Against Flu
The 1918 influenza pandemic, which affected 500 million people globally and caused 50-100 million deaths, was the most severe pandemic in recorded history. Over the course of the last 100 years, advances in science and medicine have provided the tools to address influenza much more successfully. However, despite vaccines and supportive medical interventions such as antivirals and antibiotics, influenza remains a public health problem and can be deadly for the very young, the elderly, and the...
Genome properties in 2019: a new companion database to InterPro for the inference of complete functional attributes.
Automatic annotation of protein function is routinely applied to newly sequenced genomes. While this provides a fine-grained view of an organism's functional protein repertoire, proteins, more commonly function in a coordinated manner, such as in pathways or multimeric complexes. Genome Properties (GPs) define such functional entities as a series of steps, originally described by either TIGRFAMs or Pfam entries. To increase the scope of coverage, we have migrated GPs to function as a companion...
Tracking Enterovirus D68, Cause of a Polio-like Illness in Some Patients
The J. Craig Venter Institute (JCVI) has played a vital role in defining the diversity of contemporary strains of human enteroviruses by using state-of-the art sequencing technologies, bioinformatics analyses, and in vitro and in vivo modeling.
ProteoStorm: An Ultrafast Metaproteomics Database Search Framework.
Shotgun metaproteomics has the potential to reveal the functional landscape of microbial communities but lacks appropriate methods for complex samples with unknown compositions. In the absence of prior taxonomic information, tandem mass spectra would be searched against large pan-microbial databases, which requires heavy computational workload and reduces sensitivity. We present ProteoStorm, an efficient database search framework for large-scale metaproteomics studies, which identifies...
FgBud3, a Rho4-Interacting Guanine Nucleotide Exchange Factor, Is Involved in Polarity Growth, Cell Division and Pathogenicity of <i>Fusarium graminearum</i>.
Rho GTPases are signaling macromolecules that are associated with developmental progression and pathogenesis of . Generally, enzymatic activities of Rho GTPases are regulated by Rho GTPase guanine nucleotide exchange factors (RhoGEFs). In this study, we identified a putative RhoGEF encoding gene () in database and proceeded further by using a functional genetic approach to generate targeted gene deletion mutant. Phenotypic analysis results showed that the deletion of caused severe reduction...
Human Hair Microbiota
Human hair samples are an important trace evidence type for providing leads in forensic investigations. They are used to determine the race, gender, and identity of the individual responsible for a criminal act. Hair also supports its own microbial habitat that is intra- and inter-personal variable, and as such, this little explored substrate has significant potential in forensics microbiome research due to the unique signatures that are available on an individual. We explored 16S rRNA...
InterPro in 2011: new developments in the family and domain prediction database.
InterPro (http://www.ebi.ac.uk/interpro/) is a database that integrates diverse information about protein families, domains and functional sites, and makes it freely available to the public via Web-based interfaces and services. Central to the database are diagnostic models, known as signatures, against which protein sequences can be searched to determine their potential function. InterPro has utility in the large-scale analysis of whole genomes and meta-genomes, as well as in characterizing...
BorreliaBase: a phylogeny-centered browser of Borrelia genomes.
The bacterial genus Borrelia (phylum Spirochaetes) consists of two groups of pathogens represented respectively by B. burgdorferi, the agent of Lyme borreliosis, and B. hermsii, the agent of tick-borne relapsing fever. The number of publicly available Borrelia genomic sequences is growing rapidly with the discovery and sequencing of Borrelia strains worldwide. There is however a lack of dedicated online databases to facilitate comparative analyses of Borrelia genomes.
Phylogenomic identification of regulatory sequences in bacteria: an analysis of statistical power and an application to Borrelia burgdorferi sensu lato.
Phylogenomic footprinting is an approach for ab initio identification of genome-wide regulatory elements in bacterial species based on sequence conservation. The statistical power of the phylogenomic approach depends on the degree of sequence conservation, the length of regulatory elements, and the level of phylogenetic divergence among genomes. Building on an earlier model, we propose a binomial model that uses synonymous tree lengths as neutral expectations for determining the statistical...