title: Exploration of phylogenetic data using a global sequence analysis method.
abstract: BACKGROUND
  Molecular phylogenetic methods are based on alignments of nucleic or peptidic sequences. The tremendous increase in molecular data permits phylogenetic analyses of very long sequences and of many species, but also requires methods to help manage large datasets.
  
  
  RESULTS
  Here we explore the phylogenetic signal present in molecular data by genomic signatures, defined as the set of frequencies of short oligonucleotides present in DNA sequences. Although violating many of the standard assumptions of traditional phylogenetic analyses--in particular explicit statements of homology inherent in character matrices--the use of the signature does permit the analysis of very long sequences, even those that are unalignable, and is therefore most useful in cases where alignment is questionable. We compare the results obtained by traditional phylogenetic methods to those inferred by the signature method for two genes: RAG1, which is easily alignable, and 18S RNA, where alignments are often ambiguous for some regions. We also apply this method to a multigene data set of 33 genes for 9 bacteria and one archea species as well as to the whole genome of a set of 16 gamma-proteobacteria. In addition to delivering phylogenetic results comparable to traditional methods, the comparison of signatures for the sequences involved in the bacterial example identified putative candidates for horizontal gene transfers.
  
  
  CONCLUSIONS
  The signature method is therefore a fast tool for exploring phylogenetic data, providing not only a pretreatment for discovering new sequence relationships, but also for identifying cases of sequence evolution that could confound traditional phylogenetic analysis.
authors.affiliation: Equipe de Bioinformatique Génomique et Moléculaire, INSERM U 726, Case 7113, Tour 53-54, 2 Place Jussieu, 75005 Paris, France. cchapus@oeb.harvard.edu
authors.forename: Charles
authors.initials: C
authors.lastname: Chapus
authors.forename: Christine
authors.initials: C
authors.lastname: Dufraigne
authors.forename: Scott
authors.initials: S
authors.lastname: Edwards
authors.forename: Alain
authors.initials: A
authors.lastname: Giron
authors.forename: Bernard
authors.initials: B
authors.lastname: Fertil
authors.forename: Patrick
authors.initials: P
authors.lastname: Deschavanne
mesh_terms: D000465:Algorithms; D000818:Animals; D016000:Cluster Analysis; D019295:Computational Biology; D003198:Computer Simulation; D004247:DNA / Q000235:genetics; D020563:Gammaproteobacteria / Q000235:genetics; D022761:Gene Transfer, Horizontal; D017343:Genes, Plant; D016678:Genome; D018398:Homeodomain Proteins / Q000235:genetics; D006801:Humans; D015233:Models, Statistical; D005810:Multigene Family; D010802:Phylogeny; D012335:RNA, Ribosomal / Q000235:genetics; D012336:RNA, Ribosomal, 16S / Q000235:genetics; D012337:RNA, Ribosomal, 18S / Q000235:genetics; D016415:Sequence Alignment; D017421:Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software
chemical_list: D018398:Homeodomain Proteins; D012335:RNA, Ribosomal; D012336:RNA, Ribosomal, 16S; D012337:RNA, Ribosomal, 18S; C064658:RAG-1 protein; D004247:DNA