Measuring the coding potential of genomic sequences through a combination of triplet occurrence patterns and RNY preference.
The distribution of n-tuplet frequencies is shown to strongly correlate with functionality when examining a genomic sequence in a reading-frame specific manner. The approach described herein applies a coarse-graining procedure, which is able to reveal aspects of triplet usage that are related to protein coding, while at the same time remaining species independent, based on a simple summation of suitable triplet occurrences measures. These quantities are ratios of simple frequencies to suitable mononucleotide-frequency products promoting the incidence of the RNY motif, preferred in the most widely used codons. A significant distinction of coding and noncoding sequences is achieved.
Nikolaou
Christoforos
C
Institute of Biology, National Research Center for Physical Sciences Demokritos, Athens, Greece.
Almirantis
Yannis
Y
D000465:Algorithms; D003062:Codon / Q000235:genetics*; D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D008957:Models, Genetic; D009841:Oligonucleotides / Q000235:genetics*; D016366:Open Reading Frames / Q000235:genetics*; D013045:Species Specificity
D003062:Codon; D009841:Oligonucleotides