title: The purity measure for genomic regions leads to horizontally transferred genes.
abstract: Sequence analysis is important to understand a genome, and a number of approaches such as sequence alignments and hidden Markov models have been employed. In the field of text mining, the purity measure is developed to detect unusual regions of a string without any domain knowledge. It is reported in that work that only RNAs and transposons are shown to have high purity values. In this work, the purity values of regions of various bacterial genome sequences are computed, and those regions are analyzed extensively. It is found that mobile elements and phages as well as RNAs and transposons have high purity values. It is interesting that they are all classified into a group of horizontally transferred genes. This means that the purity measure is useful to predict horizontally transferred genes.
authors.affiliation: Department of Informatics, Kyushu University, Fukuoka, Japan.
authors.forename: Yuta
authors.initials: Y
authors.lastname: Taniguchi
authors.forename: Yasuhiro
authors.initials: Y
authors.lastname: Yamada
authors.forename: Osamu
authors.initials: O
authors.lastname: Maruyama
authors.forename: Satoru
authors.initials: S
authors.lastname: Kuhara
authors.forename: Daisuke
authors.initials: D
authors.lastname: Ikeda
mesh_terms: D004251:DNA Transposable Elements; D022761:Gene Transfer, Horizontal; D016680:Genome, Bacterial; D008957:Models, Genetic; D012329:RNA, Bacterial
chemical_list: D004251:DNA Transposable Elements; D012329:RNA, Bacterial