000202448 001__ 202448
000202448 005__ 20181203023633.0
000202448 0247_ $$2doi$$a10.1016/j.ygeno.2014.07.004
000202448 022__ $$a0888-7543
000202448 02470 $$2ISI$$a000341061800003
000202448 037__ $$aARTICLE
000202448 245__ $$aClassification of selectively constrained DNA elements using feature vectors and rule-based classifiers
000202448 260__ $$aSan Diego$$bAcademic Press Inc Elsevier Science$$c2014
000202448 269__ $$a2014
000202448 300__ $$a8
000202448 336__ $$aJournal Articles
000202448 520__ $$aScarce 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. (C) 2014 Elsevier Inc. All rights reserved.
000202448 6531_ $$aConserved noncoding elements (CNEs)
000202448 6531_ $$aUltraconserved elements (UCEs)
000202448 6531_ $$aClassification
000202448 6531_ $$aRule-based classifiers
000202448 6531_ $$aFeature vector representation
000202448 6531_ $$aAlignment-free classification
000202448 700__ $$aPolychronopoulos, Dimitris$$uNatl Ctr Sci Res Demokritos, Inst Biosci & Applicat, Athens 15310, Greece
000202448 700__ $$aWeitschek, Emanuel$$uRoma Tre Univ, Dept Engn, I-00146 Rome, Italy
000202448 700__ $$0243606$$aDimitrieva, Slavica$$g190564$$uSwiss Fed Inst Technol, EPFL, Sch Life Sci, Swiss Inst Expt Canc Res, CH-1015 Lausanne, Switzerland
000202448 700__ $$0244404$$aBucher, Philipp$$g113607$$uSwiss Fed Inst Technol, EPFL, Sch Life Sci, Swiss Inst Expt Canc Res, CH-1015 Lausanne, Switzerland
000202448 700__ $$aFelici, Giovanni$$uCNR, Inst Syst Anal & Comp Sci Antonio Roberti, Rome 00185, Italy
000202448 700__ $$aAlmirantis, Yannis$$uNatl Ctr Sci Res Demokritos, Inst Biosci & Applicat, Athens 15310, Greece
000202448 773__ $$j104$$k2$$q79-86$$tGenomics
000202448 909C0 $$0252244$$pGR-BUCHER$$xU11780
000202448 909CO $$ooai:infoscience.tind.io:202448$$pSV$$particle
000202448 917Z8 $$x113607
000202448 937__ $$aEPFL-ARTICLE-202448
000202448 973__ $$aEPFL$$rREVIEWED$$sPUBLISHED
000202448 980__ $$aARTICLE