BPSI2.0: A C/C++ interface program for species identification via DNA barcoding with a BP-neural network by calling the Matlab engine

Molecular Ecology Resources

Volumn 9, Issue 1, 2009, Pages 104-106

  Zhang, A B ^a   Savolainen, P ^a  

^a ALBANOVA UNIVERSITY CENTER   (Sweden)

Author keywords

C C++; DNA barcoding; Matlab engine; Neural network

Indexed keywords

EID: 58949096376     PISSN: 1755098X     EISSN: None     Source Type: Journal    
DOI: 10.1111/j.1755-0998.2008.02372.x     Document Type: Article

References (16)

1. Altschul SF, Gish W, Miller W, Meyers EW, Lipman DJ (1990) Basic local alignment search tool. Journal of Molecular Biology, 215, 03 410.
2. Altschul SF, Madden TL, Schaffer AA et al 1997) Gapped blast and psi-blast: a new generation of protein database search programs. Nucleic Acids Research, 25, 3389 3402.
3. DeSalle R, Egan MG, Siddall M (2005) The unholy trinity: taxonomy, species delimitation and DNA barcoding. Philosophical Transactions of the Royal Society B: Biological Sciences, 360, 1975 1980.
4. Ekrem T, Willassen E, Stur E (2007) A comprehensive DNA library is essential for identification with DNA barcodes. Molecular Phylogenetics and Evolution, 43, 530 542.
5. Hebert PDN, Cywinska A, Ball SL, DeWaard JR (2003a) Biological identifications through DNA barcodes. Proceedings of the Royal Society B: Biological Sciences, 270, 313 321.
6. Hebert PDN, Ratnasingham S, deWaard JR (2003b) Barcoding animal life: cytochrome c oxidase subunit 1 divergences among closely related species. Proceedings of the Royal Society B: Biological Sciences, 270 (Supplement 96 99.
7. Koski LB, Golding GB (2001) The closest blast hit is often not the nearest neighbor. Journal of Molecular Biology, 52, 540 542.
8. Schindel DE, Miller SE (2005) DNA barcoding a useful tool for taxonomists. Nature, 435, 17.
9. Steel MA, Hendy MD, Penny D (1988) Loss of information in genetic distances. Nature, 336, 118.
10. Steinke D, Vences M, Salzburger W, Meyer A (2005) Taxl - a software for DNA barcoding using distance methods. Philosophical Transactions of the Royal Society B, 360, 1975 1980.
11. Tavares ES, Baker JA (2008) Single mitochondrial gene barcodes reliably identify sister-species in diverse clades of birds. BMC Evolutionary Biology, 8, 81. doi:.
12. Ward RD, Zemlak TS, Innes BH, Last PR, Hebert PD (2005) DNA barcoding Australia's fish species. Philosophical Transactions of the Royal Society B: Biological Sciences, B360, 1847 1857.
13. Wu CH (1997) Artificial neural networks for molecular sequence analysis. Computers & Chemistry, 40, 237 256.
14. Zhang GQ, Patuwo BE, Hu MY (1998) Forecasting with artificial neural networks: the state of the art. International Journal of Forecasting, 14, 35 62.
15. Zhang AB, Sikes DS, Muster C, Li SQ (2008) Inferring species membership using DNA sequences with back-propagation neural networks. Systematic Biology, 57, 202 215.
16. Zhang AB, Wang ZJ, Li DM (2002) Application of BP model and LOGIT model to prediction of occurrence of forest insect pest. Acta Ecology Sinica, 21, 2159 2165.