Starts of bacterial genes: estimating the reliability of computer predictions

Gene. 1999 Jul 8;234(2):257-65. doi: 10.1016/s0378-1119(99)00200-0.


Exact mapping of gene starts is an important problem in the computer-assisted functional analysis of newly sequenced prokaryotic genomes. We describe an algorithm for finding ribosomal binding sites without a learning sample. This algorithm is particularly useful for analysis of genomes with little or no experimentally mapped genes. There is a clear correlation between the ribosomal binding site (RBS) properties of a given genome and the potential gene start prediction accuracy. This correlation is of considerable predictive power and may be useful for estimating the expected success of future genome analysis efforts. We also demonstrate that the RBS properties depend on the phylogenetic position of a genome.

MeSH terms

  • Algorithms
  • Base Sequence
  • Binding Sites
  • Codon, Initiator / genetics
  • DNA, Bacterial / genetics
  • DNA, Bacterial / metabolism
  • Evolution, Molecular
  • Genes, Bacterial / genetics*
  • Phylogeny
  • RNA, Bacterial / genetics
  • RNA, Ribosomal / genetics
  • Reproducibility of Results
  • Ribosomes / metabolism
  • Sequence Alignment
  • Software


  • Codon, Initiator
  • DNA, Bacterial
  • RNA, Bacterial
  • RNA, Ribosomal