Dataset Information

JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure.

ABSTRACT: JavaProtein Dossier ((J)PD) is a new concept, database and visualization tool providing one of the largest collections of the physicochemical parameters describing proteins' structure, stability, function and interaction with other macromolecules. By collecting as many descriptors/parameters as possible within a single database, we can achieve a better use of the available data and information. Furthermore, data grouping allows us to generate different parameters with the potential to provide new insights into the sequence-structure-function relationship. In (J)PD, residue selection can be performed according to multiple criteria. (J)PD can simultaneously display and analyze all the physicochemical parameters of any pair of structures, using precalculated structural alignments, allowing direct parameter comparison at corresponding amino acid positions among homologous structures. In order to focus on the physicochemical (and consequently pharmacological) profile of proteins, visualization tools (showing the structure and structural parameters) also had to be optimized. Our response to this challenge was the use of Java technology with its exceptional level of interactivity. (J)PD is freely accessible (within the Gold Sting Suite) at http://sms.cbi.cnptia.embrapa.br, http://mirrors.rcsb.org/SMS, http://trantor.bioc.columbia.edu/SMS and http://www.es.embnet.org/SMS/ (Option: (Java)Protein Dossier).

SUBMITTER: Neshich G

PROVIDER: S-EPMC441618 | biostudies-literature | 2004 Jul

REPOSITORIES: biostudies-literature

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JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure.

Neshich Goran G Rocchia Walter W Mancini Adauto L AL Yamagishi Michel E B ME Kuser Paula R PR Fileto Renato R Baudet Christian C Pinto Ivan P IP Montagner Arnaldo J AJ Palandrani Juliana F JF Krauchenco Joao N JN Torres Renato C RC Souza Savio S Togawa Roberto C RC Higa Roberto H RH

Nucleic acids research 20040701 Web Server issue

JavaProtein Dossier ((J)PD) is a new concept, database and visualization tool providing one of the largest collections of the physicochemical parameters describing proteins' structure, stability, function and interaction with other macromolecules. By collecting as many descriptors/parameters as possible within a single database, we can achieve a better use of the available data and information. Furthermore, data grouping allows us to generate different parameters with the potential to provide ne ...[more]

PMID: 15215458

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Project description:BackgroundNext-generation sequencing (NGS) has been widely used in both clinics and research. It has become the most powerful tool for diagnosing genetic disorders and investigating disease etiology through the discovery of genetic variants. Variants identified by NGS are stored in variant call format (VCF) files. However, querying and filtering VCF files are extremely difficult for researchers without programming skills. Furthermore, as the mutation data are increasing exponentially, there is an urgent need to develop tools to manage these variant data in a centralized way.MethodsThe VCF-Server was developed as a web-based visualization tool to support the interactive analysis of genetic variant data. It allows researchers and medical geneticists to manage, annotate, filter, query, and export variants in a fast and effective way.ResultsIn this study, we developed the VCF-Server, a powerful and easily accessible tool for researchers and medical geneticists to perform variant analysis. Users can query VCFs, annotate, and filter variants without knowing programming code. Once the VCF file is uploaded, VCF-Server allows users to annotate the VCF with commonly used databases or user-defined variant annotations (including variant blacklist and whitelist). Variant information in the VCF is shown visually via the interactive graphical interface. Users can filter the variants with flexible filtering rules, and the prioritized variants can be exported locally for further analysis. As VCF-Server adopts a web file system, files in the VCF-Server can be stored and managed in a centralized way. Moreover, VCF-Server allows direct web-based analysis (accessible through either desktop computers or mobile devices) as well as local deployment.ConclusionsWith an easy-to-use graphical interface, VCF-Server allows researchers with little bioinformatics background to explore and mine mutation data, which may broaden the application of NGS technology in clinics and research. The tool is freely available for use at https://www.diseasegps.org/VCF-Server?lan = eng.

Project description:BACKGROUND: Integrative and comparative analyses of multiple transcriptomics, proteomics and metabolomics datasets require an intensive knowledge of tools and background concepts. Thus, it is challenging for users to perform such analyses, highlighting the need for a single tool for such purposes. The 3Omics one-click web tool was developed to visualize and rapidly integrate multiple human inter- or intra-transcriptomic, proteomic, and metabolomic data by combining five commonly used analyses: correlation networking, coexpression, phenotyping, pathway enrichment, and GO (Gene Ontology) enrichment. RESULTS: 3Omics generates inter-omic correlation networks to visualize relationships in data with respect to time or experimental conditions for all transcripts, proteins and metabolites. If only two of three omics datasets are input, then 3Omics supplements the missing transcript, protein or metabolite information related to the input data by text-mining the PubMed database. 3Omics' coexpression analysis assists in revealing functions shared among different omics datasets. 3Omics' phenotype analysis integrates Online Mendelian Inheritance in Man with available transcript or protein data. Pathway enrichment analysis on metabolomics data by 3Omics reveals enriched pathways in the KEGG/HumanCyc database. 3Omics performs statistical Gene Ontology-based functional enrichment analyses to display significantly overrepresented GO terms in transcriptomic experiments. Although the principal application of 3Omics is the integration of multiple omics datasets, it is also capable of analyzing individual omics datasets. The information obtained from the analyses of 3Omics in Case Studies 1 and 2 are also in accordance with comprehensive findings in the literature. CONCLUSIONS: 3Omics incorporates the advantages and functionality of existing software into a single platform, thereby simplifying data analysis and enabling the user to perform a one-click integrated analysis. Visualization and analysis results are downloadable for further user customization and analysis. The 3Omics software can be freely accessed at http://3omics.cmdm.tw.

Dataset Information

JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure.

Publications

JavaProtein Dossier: a novel web-based data visualization tool for comprehensive analysis of protein structure.

Similar Datasets

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