title: Probability distribution of intersymbol distances in random symbolic sequences: Applications to improving detection of keywords in texts and of amino acid clustering in proteins.
abstract: Symbolic sequences have been extensively investigated in the past few years within the framework of statistical physics. Paradigmatic examples of such sequences are written texts, and deoxyribonucleic acid (DNA) and protein sequences. In these examples, the spatial distribution of a given symbol (a word, a DNA motif, an amino acid) is a key property usually related to the symbol importance in the sequence: The more uneven and far from random the symbol distribution, the higher the relevance of the symbol to the sequence. Thus, many techniques of analysis measure in some way the deviation of the symbol spatial distribution with respect to the random expectation. The problem is then to know the spatial distribution corresponding to randomness, which is typically considered to be either the geometric or the exponential distribution. However, these distributions are only valid for very large symbolic sequences and for many occurrences of the analyzed symbol. Here, we obtain analytically the exact, randomly expected spatial distribution valid for any sequence length and any symbol frequency, and we study its main properties. The knowledge of the distribution allows us to define a measure able to properly quantify the deviation from randomness of the symbol distribution, especially for short sequences and low symbol frequency. We apply the measure to the problem of keyword detection in written texts and to study amino acid clustering in protein sequences. In texts, we show how the results improve with respect to previous methods when short texts are analyzed. In proteins, which are typically short, we show how the measure quantifies unambiguously the amino acid clustering and characterize its spatial distribution.
authors.affiliation: Departamento de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga, 29071, Málaga, Spain.
authors.forename: Pedro
authors.initials: P
authors.lastname: Carpena
authors.affiliation: Departamento de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga, 29071, Málaga, Spain.
authors.forename: Pedro A
authors.initials: PA
authors.lastname: Bernaola-Galván
authors.affiliation: Departamento de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga, 29071, Málaga, Spain.
authors.forename: Concepción
authors.initials: C
authors.lastname: Carretero-Campos
authors.affiliation: Departamento de Física Aplicada II, E.T.S.I. de Telecomunicación, Universidad de Málaga, 29071, Málaga, Spain.
authors.forename: Ana V
authors.initials: AV
authors.lastname: Coronado
mesh_terms: D000465:Algorithms; D000595:Amino Acid Sequence; D000596:Amino Acids / Q000737:chemistry*; D016000:Cluster Analysis; D019295:Computational Biology / Q000379:methods*; D008962:Models, Theoretical; D010507:Periodicity; D011336:Probability; D011506:Proteins / Q000737:chemistry; D017421:Sequence Analysis
chemical_list: D000596:Amino Acids; D011506:Proteins