RESUMEN
The neXtProt knowledgebase (https://www.nextprot.org) is an integrative resource providing both data on human protein and the tools to explore these. In order to provide comprehensive and up-to-date data, we evaluate and add new data sets. We describe the incorporation of three new data sets that provide expression, function, protein-protein binary interaction, post-translational modifications (PTM) and variant information. New SPARQL query examples illustrating uses of the new data were added. neXtProt has continued to develop tools for proteomics. We have improved the peptide uniqueness checker and have implemented a new protein digestion tool. Together, these tools make it possible to determine which proteases can be used to identify trypsin-resistant proteins by mass spectrometry. In terms of usability, we have finished revamping our web interface and completely rewritten our API. Our SPARQL endpoint now supports federated queries. All the neXtProt data are available via our user interface, API, SPARQL endpoint and FTP site, including the new PEFF 1.0 format files. Finally, the data on our FTP site is now CC BY 4.0 to promote its reuse.
Asunto(s)
Bases de Datos de Proteínas , Bases del Conocimiento , Humanos , Internet , Espectrometría de Masas , Péptidos/química , Proteínas Quinasas/química , Proteínas Quinasas/metabolismo , Procesamiento Proteico-Postraduccional , Proteínas/química , Proteínas/genética , Proteínas/metabolismo , Análisis de Secuencia de ARN , Programas Informáticos , Tripsina , Interfaz Usuario-ComputadorRESUMEN
SUMMARY: The Feature-Viewer is a lightweight library for the visualization of biological data mapped to a protein or nucleotide sequence. It is designed for ease of use while allowing for a full customization. The library is already used by several biological data resources and allows intuitive visual mapping of a full spectra of sequence features for different usages. AVAILABILITY AND IMPLEMENTATION: The Feature-Viewer is open source, compatible with state-of-the-art development technologies and responsive, also for mobile viewing. Documentation and usage examples are available online.
Asunto(s)
Computadores , Programas InformáticosRESUMEN
The neXtProt human protein knowledgebase (https://www.nextprot.org) continues to add new content and tools, with a focus on proteomics and genetic variation data. neXtProt now has proteomics data for over 85% of the human proteins, as well as new tools tailored to the proteomics community.Moreover, the neXtProt release 2016-08-25 includes over 8000 phenotypic observations for over 4000 variations in a number of genes involved in hereditary cancers and channelopathies. These changes are presented in the current neXtProt update. All of the neXtProt data are available via our user interface and FTP site. We also provide an API access and a SPARQL endpoint for more technical applications.
Asunto(s)
Bases de Datos de Proteínas , Proteómica , Estudios de Asociación Genética , Variación Genética , Humanos , Internet , Fenotipo , Proteómica/métodos , Programas Informáticos , Navegador WebRESUMEN
SUMMARY: The neXtProt peptide uniqueness checker allows scientists to define which peptides can be used to validate the existence of human proteins, i.e. map uniquely versus multiply to human protein sequences taking into account isobaric substitutions, alternative splicing and single amino acid variants. AVAILABILITY AND IMPLEMENTATION: The pepx program is available at https://github.com/calipho-sib/pepx and can be launched from the command line or through a cgi web interface. Indexing requires a sequence file in FASTA format. The peptide uniqueness checker tool is freely available on the web at https://www.nextprot.org/tools/peptide-uniqueness-checker and from the neXtProt API at https://api.nextprot.org/. CONTACT: lydie.lane@sib.swiss.
Asunto(s)
Péptidos/análisis , Proteómica/métodos , Programas Informáticos , Bases de Datos de Proteínas , Humanos , Proteínas/análisisRESUMEN
Voltage-gated sodium channels are pore-forming transmembrane proteins that selectively allow sodium ions to flow across the plasma membrane according to the electro-chemical gradient thus mediating the rising phase of action potentials in excitable cells and playing key roles in physiological processes such as neurotransmission, skeletal muscle contraction, heart rhythm, and pain sensation. Genetic variations in the nine human genes encoding these channels are known to cause a large range of diseases affecting the nervous and cardiac systems. Understanding the molecular effect of genetic variations is critical for elucidating the pathologic mechanisms of known variations and in predicting the effect of newly discovered ones. To this end, we have created a Web-based tool, the Ion Channels Variants Portal, which compiles all variants characterized functionally in the human sodium channel genes. This portal describes 672 variants each associated with at least one molecular or clinical phenotypic impact, for a total of 4,658 observations extracted from 264 different research articles. These data were captured as structured annotations using standardized vocabularies and ontologies, such as the Gene Ontology and the Ion Channel ElectroPhysiology Ontology. All these data are available to the scientific community via neXtProt at https://www.nextprot.org/portals/navmut.