title: Classification of selectively constrained DNA elements using feature vectors and rule-based classifiers.
abstract: Scarce work has been done in the analysis of the composition of conserved non-coding elements (CNEs) that are identified by comparisons of two or more genomes and are found to exist in all metazoan genomes. Here we present the analysis of CNEs with a methodology that takes into account word occurrence at various lengths scales in the form of feature vector representation and rule based classifiers. We implement our approach on both protein-coding exons and CNEs, originating from human, insect (Drosophila melanogaster) and worm (Caenorhabditis elegans) genomes, that are either identified in the present study or obtained from the literature. Alignment free feature vector representation of sequences combined with rule-based classification methods leads to successful classification of the different CNEs classes. Biologically meaningful results are derived by comparison with the genomic signatures approach, and classification rates for a variety of functional elements of the genomes along with surrogates are presented.
authors: Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310 Athens, Greece; Department of Biochemistry and Molecular Biology, Faculty of Biology, National and Kapodistrian University of Athens, 15701 Athens, Greece. Electronic address: dpolychr@bio.demokritos.gr.
authors: Dimitris
authors: D
authors: Polychronopoulos
authors: Department of Engineering, Roma Tre University, Via della Vasca Navale 79, 00146 Rome, Italy; Institute of Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Viale Manzoni 30, 00185 Rome, Italy. Electronic address: emanuel@dia.uniroma3.it.
authors: Emanuel
authors: E
authors: Weitschek
authors: Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland. Electronic address: slavica.dimitrieva@epfl.ch.
authors: Slavica
authors: S
authors: Dimitrieva
authors: Swiss Institute for Experimental Cancer Research (ISREC), School of Life Sciences, Swiss Federal Institute of Technology (EPFL), Lausanne, Switzerland; Swiss Institute of Bioinformatics (SIB), CH-1015 Lausanne, Switzerland. Electronic address: philipp.bucher@epfl.ch.
authors: Philipp
authors: P
authors: Bucher
authors: Institute of Systems Analysis and Computer Science "Antonio Ruberti", National Research Council, Viale Manzoni 30, 00185 Rome, Italy. Electronic address: giovanni.felici@iasi.cnr.it.
authors: Giovanni
authors: G
authors: Felici
authors: Institute of Biosciences and Applications, National Center for Scientific Research "Demokritos", 15310 Athens, Greece. Electronic address: yalmir@bio.demokritos.gr.
authors: Yannis
authors: Y
authors: Almirantis
mesh_terms: D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D021901:DNA, Intergenic / Q000235:genetics*; D004331:Drosophila melanogaster / Q000235:genetics*; D019143:Evolution, Molecular; D005091:Exons; D023281:Genomics; D006801:Humans; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA / Q000379:methods*
chemical_list: D021901:DNA, Intergenic
keywords: Alignment-free classification; Classification; Conserved noncoding elements (CNEs); Feature vector representation; Rule-based classifiers; Ultraconserved elements (UCEs)