title: Statistics of N-terminal alignment as a guide for refining prokaryotic gene annotation.
abstract: Identification of a correct N-terminus of a protein is an important step in genome annotation. However, we sometimes encounter incorrectly annotated N-termini in genomic databases. We analyzed statistics of surplus or missing N-terminal amino acid residues in tentatively translated coding sequence of cyanobacterial database entries, and found that, on average, about 8-9% of the aligned proteins have a putative incorrect N-terminus, although the percentage was dependent on the database entry. In an attempt to find more plausible N-termini for these proteins, we were able to estimate a better-aligning N-terminus in 90% of the cases. TTG was found as a putative initiation codon in most cases of recessed N-termini. This statistical approach, applicable to any group of prokaryotes, will help identify a plausible translation initiation site for each protein-coding gene in newly sequenced genomes, and also is a method of refining the N-terminus of proteins in already published genomes.
authors.affiliation: Department of Life Sciences, Graduate School of Arts and Sciences, University of Tokyo, Meguro-ku, Tokyo, Japan. naokisat@bio.c.u-tokyo.ac.jp
authors.forename: Naoki
authors.initials: N
authors.lastname: Sato
authors.forename: Naoyuki
authors.initials: N
authors.lastname: Tajima
mesh_terms: D020816:Amino Acid Motifs / Q000235:genetics; D000595:Amino Acid Sequence; D018387:Codon, Initiator; D000458:Cyanobacteria / Q000235:genetics*; D030562:Databases, Protein; D016680:Genome, Bacterial; D058977:Molecular Sequence Annotation; D008969:Molecular Sequence Data; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA
chemical_list: D018387:Codon, Initiator