Partial DNA Sequence;
DNA Barcode;
Species Identification;
Machine Learning;
BARCODE;
CLASSIFICATION;
SOFTWARE;
SYSTEM;
D O I:
10.1109/BIBE.2018.00052
中图分类号:
R318 [生物医学工程];
学科分类号:
0831 ;
摘要:
Species identification with partial DNA sequences has proved effective for different organisms. DNA barcode is a short genetic marker in an organism's DNA to identify which species it belongs to. In this work, we analyze the effectiveness of supervised machine learning methods to classify species with DNA barcode. We choose specimens from phylogenetically diverse species belonging to the animal, plant and fungus kingdoms. We consider the supervised machine learning methods, simple logistic function, random forest, PART, instance-based k-nearest neighbor, attribute-based classifier, and bagging. The analysis of results on various datasets shows that the classification performances of the selected methods are encouraging, and has an accuracy of 93.66% on average. This result shows 6% improvement compared to the state-of-art DNA barcode classification methods, which have 88.37% accuracy on average.
机构:
Karpagam Acad Higher Educ, Dept CSE, Coimbatore, Tamil Nadu, IndiaKarpagam Acad Higher Educ, Dept CSE, Coimbatore, Tamil Nadu, India
Parvathy, Priyanka
Subramaniam, Kamalraj
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机构:
Karpagam Acad Higher Educ, Dept ECE, Coimbatore, Tamil Nadu, IndiaKarpagam Acad Higher Educ, Dept CSE, Coimbatore, Tamil Nadu, India
Subramaniam, Kamalraj
Venkatesan, G. K. D. Prasanna
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Karpagam Acad Higher Educ, Fac Engn, Coimbatore, Tamil Nadu, IndiaKarpagam Acad Higher Educ, Dept CSE, Coimbatore, Tamil Nadu, India
Venkatesan, G. K. D. Prasanna
Karthikaikumar, P.
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Karpagam Coll Engn, Dept CSE, Coimbatore, Tamil Nadu, IndiaKarpagam Acad Higher Educ, Dept CSE, Coimbatore, Tamil Nadu, India
Karthikaikumar, P.
Varghese, Justin
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Karpagam Coll Engn, Dept CSE, Coimbatore, Tamil Nadu, IndiaKarpagam Acad Higher Educ, Dept CSE, Coimbatore, Tamil Nadu, India
Varghese, Justin
Jayasankar, T.
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机构:
Anna Univ, Univ Coll Engn, Dept ECE, BIT Campus, Tiruchirappalli, Tamil Nadu, IndiaKarpagam Acad Higher Educ, Dept CSE, Coimbatore, Tamil Nadu, India
机构:
King Saud Univ, Coll Med, Dept Physiol, POB 2925, Riyadh 11461, Saudi Arabia
King Saud Univ, King Khalid Univ Hosp, POB 2925, Riyadh 11461, Saudi ArabiaVidyavardhaka Coll Engn, Dept Comp Sci & Engn, Mysuru 570002, Karnataka, India
Nasif, Omaima
Alharbi, Sulaiman Ali
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机构:
King Saud Univ, Coll Sci, Dept Bot & Microbiol, POB 2455, Riyadh 11451, Saudi ArabiaVidyavardhaka Coll Engn, Dept Comp Sci & Engn, Mysuru 570002, Karnataka, India