title: Support vector machine classification of streptavidin-binding aptamers.
abstract: BACKGROUND
  Synthesizing and characterizing aptamers with high affinity and specificity have been extensively carried out for analytical and biomedical applications. Few publications can be found that describe structure-activity relationships (SARs) of candidate aptamer sequences.
  
  
  METHODS
  This paper reports pattern recognition with support vector machine (SVM) classification techniques for the identification of streptavidin-binding aptamers as "low" or "high" affinity aptamers. The SVM parameters C and γ were optimized using genetic algorithms. Four descriptors, the topological descriptor PW4 (path/walk 4--Randic shape index), the connectivity index X3A (average connectivity index chi-3), the topological charge index JGI2 (mean topological charge index of order 2), and the free energy E of the secondary structure, were used to describe the structures of candidate aptamer sequences from SELEX selection (Schütze et al. (2011) PLoS ONE (12):e29604).
  
  
  CONCLUSIONS
  The predicted fractions of winning streptavidin-binding aptamers for ten rounds of SELEX conform to the aptamer evolutionary principles of SELEX-based screening. The feasibility of applying pattern recognition based on SVM and genetic algorithms for streptavidin-binding aptamers has been demonstrated.
authors.affiliation: College of Chemistry and Chemical Engineering, Hunan Institute of Engineering, Xiangtan, Hunan, China; State Key Laboratory of Chemo/Biosensing and Chemometrics, College of Chemistry and Chemical Engineering, Hunan University, Changsha, Hunan, China.
authors.forename: Xinliang
authors.initials: X
authors.lastname: Yu
authors.affiliation: G1302, Lushan International Experimental School, Changsha, Hunan, China.
authors.forename: Yixiong
authors.initials: Y
authors.lastname: Yu
authors.affiliation: Department of Neurological Surgery, Xiangtan Central Hospital, Xiangtan, Hunan, China.
authors.forename: Qun
authors.initials: Q
authors.lastname: Zeng
mesh_terms: D052157:Aptamers, Nucleotide / Q000737:chemistry; D052156:SELEX Aptamer Technique / Q000379:methods*; D019809:Streptavidin / Q000737:chemistry*; D060388:Support Vector Machine
chemical_list: D052157:Aptamers, Nucleotide; D019809:Streptavidin