title: Comment on "SCS: signal, context, and structure features for genome-wide human promoter recognition".
abstract: We comment on the flexibility profiles calculated by Zeng et al., and show that these profiles do not represent the local flexibility of the DNA molecule. If one takes into account the physics of elasticity, the averaged flexibility profile show an additional peak which is missed in the original calculation. We show that it is not possible to calculate the flexibility of a 6-mer using tetranucleotide elastic constants, the shortest sequence is a 7-mer. For 6-mers, dinucleotide or trinucleotide parameters are needed. We present calculations for dinucleotide flexibility parameters and show that the same additional peak is present for both 7-mers and 6-mers.
authors.affiliation: Federal University of Ouro Preto, Ouro Preto.
authors.forename: Denise
authors.initials: D
authors.lastname: Fagundes-Lima
authors.forename: Gerald
authors.initials: G
authors.lastname: Weber
mesh_terms: D000465:Algorithms; D023281:Genomics / Q000379:methods*; D006801:Humans; D011401:Promoter Regions, Genetic / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods*