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iDNABar: A Rapid Species Identification Toolbox for DNA Barcoding, Collection, Preservation, Identification and Tracing

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Practical Applications of Intelligent Systems

Part of the book series: Advances in Intelligent and Soft Computing ((AINSC,volume 124))

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Abstract

DNA barcoding technology, which uses of one or a few DNA fragments for rapid identification of species, is a research focus on biodiversity information studies. In this paper, a data analysis toolbox, iDNABar, is designed and implemented to support species identification with all phases of the analytical flow, form specimen collection to tightly validated barcode library for any DNA fragment. The method of identification is proposed; key elements to management and sharing are also presented, including the user security, statistical functions and application interfaces. Meanwhile, the applications of the implementation are discussed to drive the species identification cloud’s development. (For download: http://www.darwintree.cn/tools.htm)

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References

  1. Hebert, P.D.N., Cywinska, A., Ball, S.L., de Waard, J.R.: Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences 270, 313–321 (2003)

    Article  Google Scholar 

  2. Schindel, D., Miller, S.E.: DNA barcoding a useful tool for taxonomists. Nature (2005)

    Google Scholar 

  3. Ratnasingham, S., Hebert, P.D.N.: BOLD: The Barcode of Life Data System. Molecular Ecology Notes 7, 355–364 (2007), http://www.barcodinglife.org

  4. Ward, R., Hanner, R., Hebert, P.: The campaign to DNA barcode all fishes, FISH-BOL. Journal of Fish Biology 74, 329–356 (2009)

    Article  Google Scholar 

  5. von Stackelberg, M., Rensing, S.A., Resk, R.: Identification of genic moss SSR markers and a comparative analysis of twenty-four algal and plant gene indices reveal species-specific rather than group-specific characteristics of microsatellites. BMC Plant Biol. 6, 9 (2006)

    Article  Google Scholar 

  6. Nhung, P.H., Shah, M.M., Ohkusu, K., Noda, M., Hata, H., Sun, X.S., Iihara, H., Goto, K., Masaki, T., Miyasaka, J., Ezaki, T.: The dnaJ gene as a novel phylogenetic marker for identification of Vibrio species. Syst. Appl. Microbiol. 30, 309–315 (2007)

    Article  Google Scholar 

  7. Clerc-Blain, J.L., Starr, J.R., Bull, R.D., Saarela, J.M.: A regional approach to plant DNA barcoding provides high species resolution of sedges (Carex and Kobresia, Cyperaceae) in the Canadian Arctic Archipelago. Mol. Ecol. Resour. 10, 69–91 (2010)

    Article  Google Scholar 

  8. Erickson, D.L., Spouge, J., Resch, A., Weigt, L.A., Kress, W.J.: DNA barcoding in land plants: developing standards to quantify and maximize success. Taxon 57, 1304 (2008)

    Google Scholar 

  9. Benson, D.A., Karsch-Mizrachi, I., Lipman, D.J., Ostell, J., Sayers, E.W.: GenBank. Nucleic Acids Research 37, 26–31 (2009)

    Article  Google Scholar 

  10. Meng, Z., Lin, X., He, X., Gao, Y., Liu, H., Liu, Y., Zhou, Y., Li, J., Chen, Z., Zhang, S.: Construction of the Platform for Phylogenetic Analysis, Data Driven e-Science, pp. 507–514. Springer Science+ Business Media (2011)

    Google Scholar 

  11. Altschul, S.F., Madden, T.L., Sch́ffer, A.A., Zhang, J., Zhang, Z., Miller, W., Lipman, D.J.: Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Research 25, 33–89 (1997)

    Article  Google Scholar 

  12. Ewing, B., Hillier, L.D., Wendl, M.C., Green, P.: Base-calling of automated sequencer traces usingPhred. I. Accuracy assessment. Genome Research 8, 175 (1998)

    Google Scholar 

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© 2011 Springer-Verlag Berlin Heidelberg

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Meng, Z., Li, J., Zhou, Y., Gao, Y., Shen, Z. (2011). iDNABar: A Rapid Species Identification Toolbox for DNA Barcoding, Collection, Preservation, Identification and Tracing. In: Wang, Y., Li, T. (eds) Practical Applications of Intelligent Systems. Advances in Intelligent and Soft Computing, vol 124. Springer, Berlin, Heidelberg. https://doi.org/10.1007/978-3-642-25658-5_42

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  • DOI: https://doi.org/10.1007/978-3-642-25658-5_42

  • Publisher Name: Springer, Berlin, Heidelberg

  • Print ISBN: 978-3-642-25657-8

  • Online ISBN: 978-3-642-25658-5

  • eBook Packages: EngineeringEngineering (R0)

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