Prokaryotic gene finding based on physicochemical characteristics of codons calculated from molecular dynamics simulations.

ABSTRACT: An ab initio model for gene prediction in prokaryotic genomes is proposed based on physicochemical characteristics of codons calculated from molecular dynamics (MD) simulations. The model requires a specification of three calculated quantities for each codon: the double-helical trinucleotide base pairing energy, the base pair stacking energy, and an index of the propensity of a codon for protein-nucleic acid interactions. The base pairing and stacking energies for each codon are obtained from recently reported MD simulations on all unique tetranucleotide steps, and the third parameter is assigned based on the conjugate rule previously proposed to account for the wobble hypothesis with respect to degeneracies in the genetic code. The third interaction propensity parameter values correlate w

SUBMITTER: Singhal P 

PROVIDER: S-EPMC2480686 | biostudies-literature | 2008 Jun

REPOSITORIES: biostudies-literature