title: On fuzzy semantic similarity measure for DNA coding.
abstract: A coding measure scheme numerically translates the DNA sequence to a time domain signal for protein coding regions identification. A number of coding measure schemes based on numerology, geometry, fixed mapping, statistical characteristics and chemical attributes of nucleotides have been proposed in recent decades. Such coding measure schemes lack the biologically meaningful aspects of nucleotide data and hence do not significantly discriminate coding regions from non-coding regions. This paper presents a novel fuzzy semantic similarity measure (FSSM) coding scheme centering on FSSM codons׳ clustering and genetic code context of nucleotides. Certain natural characteristics of nucleotides i.e. appearance as a unique combination of triplets, preserving special structure and occurrence, and ability to own and share density distributions in codons have been exploited in FSSM. The nucleotides׳ fuzzy behaviors, semantic similarities and defuzzification based on the center of gravity of nucleotides revealed a strong correlation between nucleotides in codons. The proposed FSSM coding scheme attains a significant enhancement in coding regions identification i.e. 36-133% as compared to other existing coding measure schemes tested over more than 250 benchmarked and randomly taken DNA datasets of different organisms.
authors.affiliation: College of Computer Sciences, King Faisal University, Saudi Arabia. Electronic address: mmalik@kfu.edu.sa.
authors.forename: Muneer
authors.initials: M
authors.lastname: Ahmad
authors.affiliation: Department of Computer Sciences, University Technology PETRONAS, Malaysia. Electronic address: lowtanjung@petronas.com.my.
authors.forename: Low Tang
authors.initials: LT
authors.lastname: Jung
authors.affiliation: College of Computer Sciences, King Faisal University, Saudi Arabia. Electronic address: mbhuiyan@kfu.edu.sa.
authors.forename: Md Al-Amin
authors.initials: MA
authors.lastname: Bhuiyan
mesh_terms: D003062:Codon / Q000235:genetics*; D004247:DNA / Q000235:genetics*; D030561:Databases, Nucleic Acid; D017143:Fuzzy Logic; D012660:Semantics
chemical_list: D003062:Codon; D004247:DNA
keywords: 1/f noise; 3-base periodicity; Coding measure scheme; Codons׳ clustering; Digital signal processing; Fuzzy semantic similarity