Comparative approach to correction of annotated gene starts in complete bacterial genomes

M. V. Baitalyuk, M. S. Gelfand, A. A. Mironov

Research output: Contribution to journalArticlepeer-review


A method for refining the beginnings of genes and a search for shifts of the reading frame is proposed. The method is based on a comparison of nucleotide and amino acid sequences of homologous genes of related organisms. The algorithm is based on the fact that the rate of changes in the protein-coding regions of the genome is substantially lower than that of noncoding regions. A modification of the Smith-Waterman algorithm is proposed, which makes it possible to allign the amino acid sequences obtained by formal translation of the starting nucleotide sequences by taking into account a possible shift of the reading frame. The algorithm has been implemented in the package of ORTOLOGATOR-GeneCorrector programs. Testing the program showed that the approach enables one to detect a wrong annotation of the beginnings in 1% of genes (even in well-studied organisms such as Escheriehia coli) and identify several (∼ 10) shifts of the open reading frame. Thus, the algorithm can be used at both the initial and final stages of analysis of the genome.

Original languageEnglish
Number of pages1
Issue number2
Publication statusPublished - Mar 2002
Externally publishedYes


  • Computer analysis
  • Gene
  • Genomics
  • Reading frame
  • Recognition of genes
  • Start of translation


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