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      The Bio-Community Perl toolkit for microbial ecology

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      Author(s): 1 , * , 2 , 1
      Publication date (Electronic):
      Journal: Bioinformatics
      Publisher: Oxford University Press

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          Abstract

          Summary: The development of bioinformatic solutions for microbial ecology in Perl is limited by the lack of modules to represent and manipulate microbial community profiles from amplicon and meta-omics studies. Here we introduce Bio-Community, an open-source, collaborative toolkit that extends BioPerl. Bio-Community interfaces with commonly used programs using various file formats, including BIOM, and provides operations such as rarefaction and taxonomic summaries. Bio-Community will help bioinformaticians to quickly piece together custom analysis pipelines and develop novel software.

          Availability an implementation: Bio-Community is cross-platform Perl code available from http://search.cpan.org/dist/Bio-Community under the Perl license. A readme file describes software installation and how to contribute.

          Contact: f.angly@ 123456uq.edu.au

          Supplementary information: Supplementary data are available at Bioinformatics online

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          The Bioperl toolkit: Perl modules for the life sciences.

          Jason E Stajich, David Block, Kris Boulez … (2002)
          The Bioperl project is an international open-source collaboration of biologists, bioinformaticians, and computer scientists that has evolved over the past 7 yr into the most comprehensive library of Perl modules available for managing and manipulating life-science information. Bioperl provides an easy-to-use, stable, and consistent programming interface for bioinformatics application programmers. The Bioperl modules have been successfully and repeatedly used to reduce otherwise complex tasks to only a few lines of code. The Bioperl object model has been proven to be flexible enough to support enterprise-level applications such as EnsEMBL, while maintaining an easy learning curve for novice Perl programmers. Bioperl is capable of executing analyses and processing results from programs such as BLAST, ClustalW, or the EMBOSS suite. Interoperation with modules written in Python and Java is supported through the evolving BioCORBA bridge. Bioperl provides access to data stores such as GenBank and SwissProt via a flexible series of sequence input/output modules, and to the emerging common sequence data storage format of the Open Bioinformatics Database Access project. This study describes the overall architecture of the toolkit, the problem domains that it addresses, and gives specific examples of how the toolkit can be used to solve common life-sciences problems. We conclude with a discussion of how the open-source nature of the project has contributed to the development effort.
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            Metagenomics: application of genomics to uncultured microorganisms.

            Jo Handelsman (2004)
            Metagenomics (also referred to as environmental and community genomics) is the genomic analysis of microorganisms by direct extraction and cloning of DNA from an assemblage of microorganisms. The development of metagenomics stemmed from the ineluctable evidence that as-yet-uncultured microorganisms represent the vast majority of organisms in most environments on earth. This evidence was derived from analyses of 16S rRNA gene sequences amplified directly from the environment, an approach that avoided the bias imposed by culturing and led to the discovery of vast new lineages of microbial life. Although the portrait of the microbial world was revolutionized by analysis of 16S rRNA genes, such studies yielded only a phylogenetic description of community membership, providing little insight into the genetics, physiology, and biochemistry of the members. Metagenomics provides a second tier of technical innovation that facilitates study of the physiology and ecology of environmental microorganisms. Novel genes and gene products discovered through metagenomics include the first bacteriorhodopsin of bacterial origin; novel small molecules with antimicrobial activity; and new members of families of known proteins, such as an Na(+)(Li(+))/H(+) antiporter, RecA, DNA polymerase, and antibiotic resistance determinants. Reassembly of multiple genomes has provided insight into energy and nutrient cycling within the community, genome structure, gene function, population genetics and microheterogeneity, and lateral gene transfer among members of an uncultured community. The application of metagenomic sequence information will facilitate the design of better culturing strategies to link genomic analysis with pure culture studies.
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              Measuring Biological Diversity

              A. E. Magurran, A.E. MAGURRAN, AE Magurran … (2004)
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                Author and article information

                Journal
                Journal ID (nlm-ta): Bioinformatics
                Journal ID (iso-abbrev): Bioinformatics
                Journal ID (publisher-id): bioinformatics
                Journal ID (hwp): bioinfo
                Title: Bioinformatics
                Publisher: Oxford University Press
                ISSN (Print): 1367-4803
                ISSN (Electronic): 1367-4811
                Publication date (Print): 01 July 2014
                Publication date (Electronic): 10 March 2014
                Publication date PMC-release: 10 March 2014
                Volume: 30
                Issue: 13
                Pages: 1926-1927
                Affiliations
                1Australian Centre for Ecogenomics, School of Chemistry and Molecular Biosciences, Level 5, Molecular Biosciences Building (76), The University of Queensland, Brisbane St Lucia, QLD 4072, Australia and 2HPCBio, Carver Biotechnology Center, Institute for Genomic Biology, 1206 West Gregory Drive | MC-195, Urbana, IL 61801, USA
                Author notes
                *To whom correspondence should be addressed.

                Associate Editor: John Hancock

                Article
                Publisher ID: btu130
                DOI: 10.1093/bioinformatics/btu130
                PMC ID: 4071200
                PubMed ID: 24618462
                SO-VID: 239ac58e-c2c0-41cf-844a-2527936eab92
                Copyright © © The Author 2014. Published by Oxford University Press.
                License:

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

                History
                Date received : 28 November 2013
                Date revision received : 29 January 2014
                Date accepted : 02 March 2014
                Page count
                Pages: 2
                Categories
                Subject: Applications Notes
                Subject: Sequence Analysis

                ScienceOpen disciplines: Bioinformatics & Computational biology
                Data availability:
                ScienceOpen disciplines: Bioinformatics & Computational biology

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