title: A whole genome study and identification of specific carcinogenic regions of the human papilloma viruses.
abstract: In this article, we undertake a study of the evolution of human papillomaviruses (HPV), whose potential to cause cervical cancer is well known. First, we found that the existing HPV groups are monophyletic and that the high risk of carcinogenicity taxa are usually clustered together. Then, we present a new algorithm for analyzing the information content of multiple sequence alignments in relation to epidemiologic carcinogenicity data to identify regions that would warrant additional experimental analyses. The new algorithm is based on a sliding window procedure and a p-value computation to identify genomic regions that are specific to HPVs causing disease. Examination of the genomes of 83 HPVs allowed us to identify specific regions that might be influenced by insertions, by deletions, or simply by mutations, and that may be of interest for further analyses. Supplementary Material is provided (see online Supplementary Material at www.libertonline.com ).
authors.affiliation: Département d'informatique, Université du Québec à Montréal, Succursale Centre-Ville, Montréal, Québec, Canada. diallo.abdoulaye@uqam.ca
authors.forename: Abdoulaye Baniré
authors.initials: AB
authors.lastname: Diallo
authors.forename: Dunarel
authors.initials: D
authors.lastname: Badescu
authors.forename: Mathieu
authors.initials: M
authors.lastname: Blanchette
authors.forename: Vladimir
authors.initials: V
authors.lastname: Makarenkov
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002472:Cell Transformation, Viral / Q000235:genetics*; D005260:Female; D015894:Genome, Human; D016679:Genome, Viral; D006801:Humans; D008957:Models, Genetic; D008969:Molecular Sequence Data; D027383:Papillomaviridae / Q000145:classification / Q000235:genetics* / Q000472:pathogenicity*; D030361:Papillomavirus Infections / Q000235:genetics* / Q000821:virology; D010802:Phylogeny; D016415:Sequence Alignment; D002583:Uterine Cervical Neoplasms / Q000235:genetics / Q000821:virology