Dataset Information

CBMAR: a comprehensive ?-lactamase molecular annotation resource.

ABSTRACT: ?-Lactam antibiotics are among the most widely used antibiotics against microbial pathogens. However, enzymatic hydrolysis of these antibiotics by bacterial ?-lactamases is increasingly compromising their efficiency. Although new generation ?-lactam antibiotics have been developed to combat antibiotic resistance, ?-lactamases have also evolved along with the new variants of the substrate. A strong selection pressure from the newer generation of ?-lactam antibiotics has resulted in evolution of different families within each class of ?-lactamase. To facilitate detailed characterization of different families of ?-lactamases, we have created a database, CBMAR, which facilitates comprehensive molecular annotation and discovery of novel ?-lactamases. As against the limited scope of other existing similar databases, CBMAR provides information useful for molecular and biochemical characterization of each family of ?-lactamase. The basic architecture of CBMAR is based on Ambler classification, which divides ?-lactamases as serine (Classes A, C and D) and metallo-?-lactamases (Class B). Each class is further divided into several families on the basis of their hydrolytic character. In CBMAR, each family is annotated with (i) sequence variability, (ii) antibiotic resistance profile, (iii) inhibitor susceptibility, (iv) active site, (v) family fingerprints, (vi) mutational profile, (vii) variants, (viii) gene location, (ix) phylogenetic tree and several other features. Each entry also has external links to the relevant protein/nucleotide sequence and structure databases. The database also supports sequence similarity searches using BLAST and assigns a new ?-lactamase protein to its respective family on the basis of family-specific fingerprint. Database URL: http://14.139.227.92/mkumar/lactamasedb

SUBMITTER: Srivastava A

PROVIDER: S-EPMC4255060 | biostudies-literature | 2014

REPOSITORIES: biostudies-literature

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CBMAR: a comprehensive β-lactamase molecular annotation resource.

Srivastava Abhishikha A Singhal Neelja N Goel Manisha M Virdi Jugsharan Singh JS Kumar Manish M

Database : the journal of biological databases and curation 20141203

β-Lactam antibiotics are among the most widely used antibiotics against microbial pathogens. However, enzymatic hydrolysis of these antibiotics by bacterial β-lactamases is increasingly compromising their efficiency. Although new generation β-lactam antibiotics have been developed to combat antibiotic resistance, β-lactamases have also evolved along with the new variants of the substrate. A strong selection pressure from the newer generation of β-lactam antibiotics has resulted in evolution of d ...[more]

PMID: 25475113

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Project description:PurposeInterpretation of genomic variants in tumor samples still presents a challenge in research and the clinical setting. A major issue is that information for variant interpretation is fragmented across disparate databases, and aggregation of information from these requires building extensive infrastructure. To this end, we have developed Genome Nexus, a one-stop shop for variant annotation with a user-friendly interface for cancer researchers and clinicians.MethodsGenome Nexus (1) aggregates variant information from sources that are relevant to cancer research and clinical applications, (2) allows high-performance programmatic access to the aggregated data via a unified application programming interface, (3) provides a reference page for individual cancer variants, (4) provides user-friendly tools for annotating variants in patients, and (5) is freely available under an open source license and can be installed in a private cloud or local environment and integrated with local institutional resources.ResultsGenome Nexus is available at https://www.genomenexus.org. It displays annotations from more than a dozen resources including those that provide variant effect information (variant effect predictor), protein sequence annotation (Uniprot, Pfam, and dbPTM), functional consequence prediction (Polyphen-2, Mutation Assessor, and SIFT), population prevalences (gnomAD, dbSNP, and ExAC), cancer population prevalences (Cancer hotspots and SignalDB), and clinical actionability (OncoKB, CIViC, and ClinVar). We describe several use cases that demonstrate the utility of Genome Nexus to clinicians, researchers, and bioinformaticians. We cover single-variant annotation, cohort analysis, and programmatic use of the application programming interface. Genome Nexus is unique in providing a user-friendly interface specific to cancer that allows high-performance annotation of any variant including unknown ones.ConclusionInterpretation of cancer genomic variants is improved tremendously by having an integrated resource for annotations. Genome Nexus is freely available under an open source license.

Dataset Information

CBMAR: a comprehensive ?-lactamase molecular annotation resource.

Publications

CBMAR: a comprehensive β-lactamase molecular annotation resource.

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