title: A dictionary based informational genome analysis.
abstract: BACKGROUND
  In the post-genomic era several methods of computational genomics are emerging to understand how the whole information is structured within genomes. Literature of last five years accounts for several alignment-free methods, arisen as alternative metrics for dissimilarity of biological sequences. Among the others, recent approaches are based on empirical frequencies of DNA k-mers in whole genomes.
  
  
  RESULTS
  Any set of words (factors) occurring in a genome provides a genomic dictionary. About sixty genomes were analyzed by means of informational indexes based on genomic dictionaries, where a systemic view replaces a local sequence analysis. A software prototype applying a methodology here outlined carried out some computations on genomic data. We computed informational indexes, built the genomic dictionaries with different sizes, along with frequency distributions. The software performed three main tasks: computation of informational indexes, storage of these in a database, index analysis and visualization. The validation was done by investigating genomes of various organisms. A systematic analysis of genomic repeats of several lengths, which is of vivid interest in biology (for example to compute excessively represented functional sequences, such as promoters), was discussed, and suggested a method to define synthetic genetic networks.
  
  
  CONCLUSIONS
  We introduced a methodology based on dictionaries, and an efficient motif-finding software application for comparative genomics. This approach could be extended along many investigation lines, namely exported in other contexts of computational genomics, as a basis for discrimination of genomic pathologies.
authors.affiliation: Department of Computer Science, Strada Le Grazie 15, 37134 Verona, Italy.
authors.forename: Alberto
authors.initials: A
authors.lastname: Castellini
authors.forename: Giuditta
authors.initials: G
authors.lastname: Franco
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Manca
mesh_terms: D000465:Algorithms; D000818:Animals; D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D003201:Computers; D004269:DNA, Bacterial / Q000032:analysis; D004271:DNA, Fungal / Q000032:analysis; D016054:DNA, Protozoan / Q000032:analysis; D030541:Databases, Genetic; D016678:Genome / Q000235:genetics*; D015698:Genomic Library; D023281:Genomics / Q000379:methods*; D006801:Humans; D007257:Information Theory; D059372:Nucleotide Motifs / Q000235:genetics; D017422:Sequence Analysis, DNA; D012984:Software
chemical_list: D004269:DNA, Bacterial; D004271:DNA, Fungal; D016054:DNA, Protozoan