A TRANSCRIPTION FRAME-BASED ANALYSIS OF THE GENOMIC DNA-SEQUENCE OF AHYPER-THERMOPHILIC ARCHAEON FOR THE IDENTIFICATION OF GENES, PSEUDO-GENES AND OPERON STRUCTURES

An algorithm for identifying transcription units, independently regula ted genes and operons, and pseudo-genes that are not expected to be ex pressed, has been developed by combining a system for predicting trans cription and translation signals, and a system for scoring the triplet periodicity in ORF candidates. By using the algorithm, the 1.09 Mb se quence that covers approximately 60% of the genome of Pyrococcus sp, O T3 has been analyzed. The identified ORFs show the expected biological and physical characteristics. while the rejected ORF candidates do no t. Frequent use of operon structures for transcription, and gene dupli cation followed by mutation or termination of the duplicated genes, ar e discussed. (C) 1998 Federation of European Biochemical Societies.