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      bold: The Barcode of Life Data System ( http://www.barcodinglife.org)

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          Abstract

          The Barcode of Life Data System ( bold) is an informatics workbench aiding the acquisition, storage, analysis and publication of DNA barcode records. By assembling molecular, morphological and distributional data, it bridges a traditional bioinformatics chasm. bold is freely available to any researcher with interests in DNA barcoding. By providing specialized services, it aids the assembly of records that meet the standards needed to gain BARCODE designation in the global sequence databases. Because of its web-based delivery and flexible data security model, it is also well positioned to support projects that involve broad research alliances. This paper provides a brief introduction to the key elements of bold, discusses their functional capabilities, and concludes by examining computational resources and future prospects.

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          Basic local alignment search tool.

          Stephen F Altschul, Warren Gish, Webb Miller … (1990)
          A new approach to rapid sequence comparison, basic local alignment search tool (BLAST), directly approximates alignments that optimize a measure of local similarity, the maximal segment pair (MSP) score. Recent mathematical results on the stochastic properties of MSP scores allow an analysis of the performance of this method as well as the statistical significance of alignments it generates. The basic algorithm is simple and robust; it can be implemented in a number of ways and applied in a variety of contexts including straightforward DNA and protein sequence database searches, motif searches, gene identification searches, and in the analysis of multiple regions of similarity in long DNA sequences. In addition to its flexibility and tractability to mathematical analysis, BLAST is an order of magnitude faster than existing sequence comparison tools of comparable sensitivity.
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            Profile hidden Markov models.

            S. Eddy (1998)
            The recent literature on profile hidden Markov model (profile HMM) methods and software is reviewed. Profile HMMs turn a multiple sequence alignment into a position-specific scoring system suitable for searching databases for remotely homologous sequences. Profile HMM analyses complement standard pairwise comparison methods for large-scale sequence analysis. Several software implementations and two large libraries of profile HMMs of common protein domains are available. HMM methods performed comparably to threading methods in the CASP2 structure prediction exercise.
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              Biological identifications through DNA barcodes.

              Paul Hebert, Alina Cywinska, Shelley Ball … (2003)
              Although much biological research depends upon species diagnoses, taxonomic expertise is collapsing. We are convinced that the sole prospect for a sustainable identification capability lies in the construction of systems that employ DNA sequences as taxon 'barcodes'. We establish that the mitochondrial gene cytochrome c oxidase I (COI) can serve as the core of a global bioidentification system for animals. First, we demonstrate that COI profiles, derived from the low-density sampling of higher taxonomic categories, ordinarily assign newly analysed taxa to the appropriate phylum or order. Second, we demonstrate that species-level assignments can be obtained by creating comprehensive COI profiles. A model COI profile, based upon the analysis of a single individual from each of 200 closely allied species of lepidopterans, was 100% successful in correctly identifying subsequent specimens. When fully developed, a COI identification system will provide a reliable, cost-effective and accessible solution to the current problem of species identification. Its assembly will also generate important new insights into the diversification of life and the rules of molecular evolution.
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                Author and article information

                Journal
                Journal ID (nlm-ta): Mol Ecol Notes
                Journal ID (publisher-id): men
                Title: Molecular Ecology Notes
                Publisher: Blackwell Publishing Ltd
                ISSN (Print): 1471-8278
                ISSN (Electronic): 1471-8286
                Publication date (Print): 01 May 2007
                Volume: 7
                Issue: 3
                Pages: 355-364
                Affiliations
                Canadian Centre for DNA Barcoding, Biodiversity Institute of Ontario, University of Guelph Guelph, ON, Canada N1G 2W1
                Author notes
                Correspondence: Paul Hebert, Fax: 519-767-1656. E-mail: phebert@ 123456uoguelph.ca
                Article
                DOI: 10.1111/j.1471-8286.2007.01678.x
                PMC ID: 1890991
                PubMed ID: 18784790
                SO-VID: 731bb5b5-7039-4023-82cb-359493f34d26
                Copyright © © 2007 The Authors Journal compilation © 2007 Blackwell Publishing Ltd
                History
                Date received : 30 July 2006
                Date accepted : 17 November 2006
                Categories
                Subject: Barcodings

                ScienceOpen disciplines: Ecology
                Keywords: coi,taxonomy,dna barcoding,informatics,species identification,gene sequence
                Data availability:
                ScienceOpen disciplines: Ecology
                Keywords: coi, taxonomy, dna barcoding, informatics, species identification, gene sequence

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