The Biological Reference Repository (BioR): a rapid and flexible system for genomics annotation
| Autor: | Steven N. Hart, Raymond Moore, Jean-Pierre A. Kocher, Valentin Dinu, Patrick H. Duffy, Daniel J. Quest, David N. Rider, Michael A. Meiners, Asif Hossain |
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| Rok vydání: | 2014 |
| Předmět: |
Statistics and Probability
Java Computer science Interface (Java) Flat file database Genomics Genome Analysis Biochemistry Applications Notes Computer Science Applications World Wide Web Computational Mathematics Annotation Computational Theory and Mathematics Software Design Perl Molecular Biology computer computer.programming_language |
| Zdroj: | Bioinformatics |
| ISSN: | 1367-4811 |
| Popis: | Motivation: The Biological Reference Repository (BioR) is a toolkit for annotating variants. BioR stores public and user-specific annotation sources in indexed JSON-encoded flat files (catalogs). The BioR toolkit provides the functionality to combine and retrieve annotation from these catalogs via the command-line interface. Several catalogs from commonly used annotation sources and instructions for creating user-specific catalogs are provided. Commands from the toolkit can be combined with other UNIX commands for advanced annotation processing. We also provide instructions for the development of custom annotation pipelines. Availability and implementation: The package is implemented in Java and makes use of external tools written in Java and Perl. The toolkit can be executed on Mac OS X 10.5 and above or any Linux distribution. The BioR application, quickstart, and user guide documents and many biological examples are available at http://bioinformaticstools.mayo.edu . Contact: Kocher.JeanPierre@mayo.edu Supplementary information: Supplementary data are available at Bioinformatics online. |
| Databáze: | OpenAIRE |
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