title: Key for protein coding sequences identification: computer analysis of codon strategy.
abstract: The signal qualifying an AUG or GUG as an initiator in mRNAs processed by E. coli ribosomes is not found to be a systematic, literal homology sequence. In contrast, stability analysis reveals that initiators always occur within nucleic acid domains of low stability, for which a high A/U content is observed. Since no aminoacid selection pressure can be detected at N-termini of the proteins, the A/U enrichment results from a biased usage of the code degeneracy. A computer analysis is presented which allows easy detection of the codon strategy. N-terminal codons carry rather systematically A or U in third position, which suggests a mechanism for translation initiation and helps to detect protein coding sequences in sequenced DNA.
mesh_terms: D000595:Amino Acid Sequence; D001426:Bacterial Proteins / Q000235:genetics*; D001483:Base Sequence; D003062:Codon / Q000235:genetics*; D003090:Coliphages / Q000235:genetics; D003201:Computers; D004269:DNA, Bacterial / Q000235:genetics*; D004926:Escherichia coli / Q000378:metabolism; D005796:Genes; D008722:Methods; D014176:Protein Biosynthesis; D012333:RNA, Messenger / Q000235:genetics*; D012270:Ribosomes / Q000378:metabolism
chemical_list: D001426:Bacterial Proteins; D003062:Codon; D004269:DNA, Bacterial; D012333:RNA, Messenger