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

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          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: peter@ 123456biomatters.com

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          Most cited references4

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          Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences

          Increased reliance on computational approaches in the life sciences has revealed grave concerns about how accessible and reproducible computation-reliant results truly are. Galaxy http://usegalaxy.org, an open web-based platform for genomic research, addresses these problems. Galaxy automatically tracks and manages data provenance and provides support for capturing the context and intent of computational methods. Galaxy Pages are interactive, web-based documents that provide users with a medium to communicate a complete computational analysis.
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            Open software for biologists: from famine to feast.

            Developing and deploying specialized computing systems for specific research communities is achievable, cost effective and has wide-ranging benefits.
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              Vector NTI, a balanced all-in-one sequence analysis suite.

              Vector NTI is a well-balanced desktop application integrated for molecular sequence analysis and biological data management. It has a centralised database and five application modules: Vector NTI, AlignX, BioAnnotator, ContigExpress and GenomBench. In this review, the features and functions available in this software are examined. These include database management, primer design, virtual cloning, alignments, sequence assembly, 3D molecular viewer and internet tools. Some problems encountered when using this software are also discussed. It is hoped that this review will introduce this software to more molecular biologists so they can make better-informed decisions when choosing computational tools to facilitate their everyday laboratory work. This tool can save time and enhance analysis but it requires some learning on the user's part and there are some issues that need to be addressed by the developer.
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                Author and article information

                Journal
                Bioinformatics
                Bioinformatics
                bioinformatics
                bioinfo
                Bioinformatics
                Oxford University Press
                1367-4803
                1367-4811
                15 June 2012
                27 April 2012
                27 April 2012
                : 28
                : 12
                : 1647-1649
                Affiliations
                1Biomatters 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
                Author notes
                * To whom correspondence should be addressed.

                Associate Editor: Alfonso Valencia

                Article
                bts199
                10.1093/bioinformatics/bts199
                3371832
                22543367
                dc15a37a-fb06-4370-ae17-16ca17c3aa01
                © The Author(s) 2012. Published by Oxford University Press.

                This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License ( http://creativecommons.org/licenses/by-nc/3.0), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

                Page count
                Pages: 3
                Categories
                Applications Note
                Sequence Analysis

                Bioinformatics & Computational biology
                Bioinformatics & Computational biology

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