title: A method for identification of highly conserved elements and evolutionary analysis of superphylum Alveolata.
abstract: BACKGROUND
  Perfectly or highly conserved DNA elements were found in vertebrates, invertebrates, and plants by various methods. However, little is known about such elements in protists. The evolutionary distance between apicomplexans can be very high, in particular, due to the positive selection pressure on them. This complicates the identification of highly conserved elements in alveolates, which is overcome by the proposed algorithm.
  
  
  RESULTS
  A novel algorithm is developed to identify highly conserved DNA elements. It is based on the identification of dense subgraphs in a specially built multipartite graph (whose parts correspond to genomes). Specifically, the algorithm does not rely on genome alignments, nor pre-identified perfectly conserved elements; instead, it performs a fast search for pairs of words (in different genomes) of maximum length with the difference below the specified edit distance. Such pair defines an edge whose weight equals the maximum (or total) length of words assigned to its ends. The graph composed of these edges is then compacted by merging some of its edges and vertices. The dense subgraphs are identified by a cellular automaton-like algorithm; each subgraph defines a cluster composed of similar inextensible words from different genomes. Almost all clusters are considered as predicted highly conserved elements. The algorithm is applied to the nuclear genomes of the superphylum Alveolata, and the corresponding phylogenetic tree is built and discussed.
  
  
  CONCLUSIONS
  We proposed an algorithm for the identification of highly conserved elements. The multitude of identified elements was used to infer the phylogeny of Alveolata.
authors.affiliation: Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia. rubanov@iitp.ru.
authors.forename: Lev I
authors.initials: LI
authors.lastname: Rubanov
authors.affiliation: Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia.
authors.forename: Alexandr V
authors.initials: AV
authors.lastname: Seliverstov
authors.affiliation: Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia.
authors.forename: Oleg A
authors.initials: OA
authors.lastname: Zverkov
authors.affiliation: Institute for Information Transmission Problems (Kharkevich Institute), Russian Academy of Sciences, Bolshoi Karetnyi per. 19, Building 1, Moscow, 127051, Russia.
authors.forename: Vassily A
authors.initials: VA
authors.lastname: Lyubetsky
mesh_terms: D000465:Algorithms; D056893:Alveolata / Q000145:classification* / Q000235:genetics*; D001483:Base Sequence; D017124:Conserved Sequence; D004247:DNA / Q000737:chemistry; D019143:Evolution, Molecular; D016678:Genome; D010802:Phylogeny; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D004247:DNA
keywords: Alveolates; Apicomplexan parasites; Dense subgraph; Highly conserved element; Phylogeny; Ultraconserved element