Primary sequences of proteins from complete genomes display a singular periodicity: Alignment-free N-gram analysis.
A method is proposed to represent and to analyze complete genome sequences (52 species from procaryotes and eukaryotes), based upon n-gram sequence's frequencies of amino acid pairs (bigrams), separated by a given number of other residues. For each of the species analyzed, it allows us to construct over-abundant and over-deficient occurrence profiles, summarizing amino acid bigram frequencies over the entire genome. The method deals efficiently with a sparseness of statistical representations of individual sequences, and describes every gene sequence in the same way, independently of its length and of the genome sizes. The frequency of over-abundant and over-deficient occurrences of bigrams presents a singular periodicity around 3.5 peptide bonds, suggesting a relation with the alpha helical secondary structure.
Radomski
Jan P
JP
Interdisciplinary Centre for Mathematical and Computational Modelling, Warsaw University, Pawińskiego 5A, Bldg. D, 02106 Warsaw, Poland. janr@icm.edu.pl
Slonimski
Piotr P
PP
D000595:Amino Acid Sequence; D001105:Archaea / Q000235:genetics; D019843:Archaeal Proteins / Q000737:chemistry / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D001426:Bacterial Proteins / Q000737:chemistry / Q000235:genetics; D016678:Genome; D011506:Proteins / Q000737:chemistry* / Q000235:genetics; D016415:Sequence Alignment; D017386:Sequence Homology, Amino Acid
D019843:Archaeal Proteins; D001426:Bacterial Proteins; D011506:Proteins