Geneious Basic: An integrated and extendable desktop software platform for the organization and analysis of sequence data

Bioinformatics (Oxford, England) - Tập 28 Số 12 - Trang 1647-1649 - 2012
Matthew D. Kearse1, Richard Moir1, Amy G. Wilson1, Steven Stones-Havas1, Matthew Cheung1, Shane Sturrock1, Simon Buxton1, Alex Cooper1, Sidney Markowitz1, Chris Duran1, Tobias Thierer1, Bruce Ashton1, Peter Meintjes1, Alexei J. Drummond1
11 Biomatters Ltd., 2/76 Anzac Avenue, Auckland, 1010, New Zealand, 2School of Agriculture and Food Science, University of Queensland, Brisbane, 4072, Australia and 3Department of Computer Science, University of Auckland, Auckland, New Zealand

Tóm tắt

Abstract Summary: The two main functions of bioinformatics are the organization and analysis of biological data using computational resources. Geneious Basic has been designed to be an easy-to-use and flexible desktop software application framework for the organization and analysis of biological data, with a focus on molecular sequences and related data types. It integrates numerous industry-standard discovery analysis tools, with interactive visualizations to generate publication-ready images. One key contribution to researchers in the life sciences is the Geneious public application programming interface (API) that affords the ability to leverage the existing framework of the Geneious Basic software platform for virtually unlimited extension and customization. The result is an increase in the speed and quality of development of computation tools for the life sciences, due to the functionality and graphical user interface available to the developer through the public API. Geneious Basic represents an ideal platform for the bioinformatics community to leverage existing components and to integrate their own specific requirements for the discovery, analysis and visualization of biological data. Availability and implementation: Binaries and public API freely available for download at http://www.geneious.com/basic, implemented in Java and supported on Linux, Apple OSX and MS Windows. The software is also available from the Bio-Linux package repository at http://nebc.nerc.ac.uk/news/geneiousonbl. Contact:  [email protected]

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Tài liệu tham khảo

Altschul, 1990, Basic local alignment search tool, J. Mol. Biol., 215, 403, 10.1016/S0022-2836(05)80360-2

Field, 2006, Open software for biologists: from famine to feast, Nat. Biotechnol., 24, 801, 10.1038/nbt0706-801

Goecks, 2010, Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences, Genome Biol., 11, R86, 10.1186/gb-2010-11-8-r86

Lu, 2004, Vector NTI, a balanced all-in-one sequence analysis suite, Brief. Bioinform., 5, 378, 10.1093/bib/5.4.378

Masters, 2011, Species Delimitation - a Geneious plugin for the exploration of species boundaries, Mol. Ecol. Resour., 11, 154, 10.1111/j.1755-0998.2010.02896.x

Schatz, 2010, Cloud computing and the DNA data race, Nat. Biotechnol., 28, 691, 10.1038/nbt0710-691

Smoot, 2010, Cytoscape 2.8: new features for data integration and network visualization, Bioinformatics, 27, 431, 10.1093/bioinformatics/btq675

Tamura, 2007, MEGA4: Molecular Evolutionary Genetics Analysis (MEGA) software version 4.0, Mol. Biol. Evol., 24, 1596, 10.1093/molbev/msm092

Thông tin
Thông tin xuất bản

Bioinformatics (Oxford, England)

Tập 28 Số 12

1647-1649

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