Advances in Genomic Sequence Analysis and Pattern Discovery PDF
Preview Advances in Genomic Sequence Analysis and Pattern Discovery
7972tp.new.indd 1 7/30/10 3:15 PM SCIENCE, ENGINEERING, AND BIOLOGY INFORMATICS Series Editor:Jason T. L. Wang (New Jersey Institute of Technology, USA) Published: Vol. 1: Advanced Analysis of Gene Expression Microarray Data (Aidong Zhang) Vol. 2: Life Science Data Mining (Stephen T. C. Wong & Chung-Sheng Li) Vol. 3: Analysis of Biological Data: A Soft Computing Approach (Sanghamitra Bandyopadhyay, Ujjwal Maulik & Jason T. L. Wang) Vol. 4: Machine Learning Approaches to Bioinformatics (Zheng Rong Yang) Vol. 5: Biodata Mining and Visualization: Novel Approaches (Ilkka Havukkala) Vol. 6: Database Technology for Life Sciences and Medicine (Claudia Plant & Christian Böhm) Vol. 7: Advances in Genomic Sequence Analysis and Pattern Discovery (Laura Elnitski, Helen Piontkivska & Lonnie R. Welch) XiaoLing - Advances in Genomic Sequence Ana2lysis.pmd 3/2/2011, 9:18 AM advances in genomic sequence analysis and pattern discovery editors Laura Elnitski National Human Genome Research Institute, National Institutes of Health, USA Helen Piontkivska Kent State University, USA Lonnie R Welch Ohio University, USA World Scientific NEW JERSEY • LONDON • SINGAPORE • BEIJING • SHANGHAI • HONG KONG • TAIPEI • CHENNAI 7972tp.new.indd 2 7/30/10 3:15 PM Published by World Scientific Publishing Co. Pte. Ltd. 5 Toh Tuck Link, Singapore 596224 USA office: 27 Warren Street, Suite 401-402, Hackensack, NJ 07601 UK office: 57 Shelton Street, Covent Garden, London WC2H 9HE British Library Cataloguing-in-Publication Data A catalogue record for this book is available from the British Library. ADVANCES IN GENOMIC SEQUENCE ANALYSIS AND PATTERN DISCOVERY Science, Engineering, and Biology Informatics — Vol. 7 Copyright © 2011 by World Scientific Publishing Co. Pte. Ltd. All rights reserved. This book, or parts thereof, may not be reproduced in any form or by any means, electronic or mechanical, including photocopying, recording or any information storage and retrieval system now known or to be invented, without written permission from the Publisher. For photocopying of material in this volume, please pay a copying fee through the Copyright Clearance Center, Inc., 222 Rosewood Drive, Danvers, MA 01923, USA. In this case permission to photocopy is not required from the publisher. ISBN-13 978-981-4327-72-5 ISBN-10 981-4327-72-7 Typeset by Stallion Press Email: [email protected] Printed in Singapore. XiaoLing - Advances in Genomic Sequence Ana1lysis.pmd 3/2/2011, 9:18 AM December16,2010 16:55 9inx6in AdvancesinGenomicSequenceAnalysisandPatternDiscovery b1051-fm Contents Preface vii AbouttheEditors ix Part I: Pattern Discovery Methods 1 Chapter1: Large-ScaleGeneRegulatoryMotifDiscovery withNestedMICA 3 MatiasPiipari,ThomasA.Down andTimJ.P.Hubbard Chapter2: R’MES:ATooltoFindMotifswithaSignificantly UnexpectedFrequencyinBiologicalSequences 25 SophieSchbathandMarkHoebeke Chapter3: AnIntricateMosaicofGenomicPatterns atMid-rangeScale 65 AlexeiFedorovandLarisaFedorova Chapter4: MotifFindingfromChipstoChIPs 93 GiulioPavesi Chapter5: ANewApproachtotheDiscoveryofRNA StructuralElementsintheHumanGenome 117 LeiHua,MiguelCervantes-Cervantes andJasonT.L.Wang Part II: Performance and Paradigms 133 Chapter6: BenchmarkingofMethodsforMotif DiscoveryinDNA 135 KjetilKlepper,GeirKjetilSandve, MortenBeckRye,KjerstiHysingBolstad andFinnDrabløs v December16,2010 16:55 9inx6in AdvancesinGenomicSequenceAnalysisandPatternDiscovery b1051-fm vi Contents Chapter7: EncyclopediasofDNAElementsforPlantGenomes 159 JensLichtenberg,AlperYilmaz,KyleKurz, XiaoyuLiang,ChaseNelson,ThomasBitterman, EricStockinger,ErichGrotewold andLonnieR.Welch Chapter8: ManycoreHigh-PerformanceComputing inBioinformatics 179 Jean-StéphaneVarré,BertilSchmidt, StéphaneJanotandMathieuGiraud Chapter9: NaturalSelectionandtheGenome 209 AustinL.Hughes Index 221 December16,2010 16:55 9inx6in AdvancesinGenomicSequenceAnalysisandPatternDiscovery b1051-fm Preface Those who are involved with mapping the genomic landscapes are participatinginoneofthemostexcitingfrontiersofscience.Wehavethe opportunitytoreverseengineertheblueprintsandthecontrolsystemsof livingorganisms.Computationaltoolsarekeyenablersinthedeciphering process.Thus,thisbookprovidesanin-depthpresentationofsomeofthe important computational biology approaches to genomic sequence anal- ysis.Thefirstpartofthebookdiscussesmethodsfordiscoveringpatterns in DNA and RNA. This is followed by the second part that reflects on methodsinvariousways,includingperformance,usageandparadigms. Part I, Pattern Discovery Methods, provides a collection of computa- tionalmethodsandtools.Chapter1,“Large-ScaleGeneRegulatoryMotif DiscoverywithNestedMICA,”presentsanalgorithmicapproach,describes usage of the tool based on the algorithm, and illustrates its usage via a detailed case study. In Chapter 2, “R’MES: A Tool to Find Motifs with a Significantly Unexpected Frequency in Biological Sequences,” the authors describe a software tool that contains rigorous statistical models of DNA words. “An Intricate Mosaic of Genomic Patterns at Mid-range Scale,” Chapter 3 of the book, focuses on intricate mosaics found in genomes; a numberofspecificpatternsareidentified.Thefourthchapter,“MotifFind- ing from Chips to ChIPs,” provides a comprehensive survey of methods forthedenovodiscoveryofputativeover-representedtranscriptionfactor bindingsitesinnucleotidesequences.PartIconcludeswithachapterthat considersthediscoveryofRNAstructuralmotifs:“ANewApproachtothe DiscoveryofRNAStructuralElementsintheHumanGenome.” The second part, Performance and Paradigms, consists of chapters thatcontemplatetheeffectivenessofrelevantcomputationalbiologytech- niques. Chapter 6, “Benchmarking of Methods for Motif Discovery in DNA,” presents a variety of metrics for assessing the performance of the class of methods described in Part I. In “Encyclopedias of DNA Ele- ments for Plant Genomes,” the application of methods is illustrated with casestudies.Thetopicofscalablealgorithmicapproachesisconsideredin vii December16,2010 16:55 9inx6in AdvancesinGenomicSequenceAnalysisandPatternDiscovery b1051-fm viii Preface Chapter 8, “Manycore High-Performance Computing in Bioinformatics.” Chapter9, “Natural Selection and the Genome,” discusses evolution of genomic sequences and the role that natural selection plays in direct- inggenomeevolution.Italsoprovidesaconceptualframeworkforbetter understandingoftheevolutionaryimplicationsandinsightsthataregen- erated through genomic sequence analyses, and emphasizes the critical roleofpurifyingselection. December16,2010 16:55 9inx6in AdvancesinGenomicSequenceAnalysisandPatternDiscovery b1051-fm About the Editors Dr. Laura Elnitski is a molecular and computational biologistwhostudiesnoncodingfunctionalelements in vertebrate genomes. She has served as an analyst for the Mouse, Rat, Chicken and Bovine Genome Consortia. Dr. Elnitski is extensively involved in NHGRI’s ENCODE(EncyclopediaofDNAElements)project, which aims to produce a comprehensive catalog of functional elements in the human genome. Dr.Elnitski’sresearchusesintegrativeanalysestoelucidateboththepres- ence and activity of functional elements in the human genome that have been historically difficult to characterize. For example, computationally, herworkpredictsmutationsincodingsequencesthataffectpropersplic- ing. Targets of these mutations include exonic splicing enhancers and silencers. In experimental analyses, she is mapping elements that silence geneexpressionusinganassaysystemdesignedinherlab. Driving towards a molecular understanding of ovarian cancer, Dr. Elnitski combines in silico and wet-bench techniques. She has anno- tatedbidirectionalpromotersinthehumangenome,includingthosereg- ulating noncoding genes, using data collected in RNA-seq assays. These results are being used to find gene silencing events caused by aberrant methylation in tumor samples. She is also addressing functional conse- quencesofmutationsinthosetumors. Dr.ElnitskiistherecipientofaRuthL.KirschsteinPostdoctoralFel- lowshipthroughtheNIH(2000–2003),OutstandingResearchAchieve- ment Award (International Symposium on Bioinformatics Research and Applications—2007),afeaturedscientistintheWomeninBioinformatics Researchdocumentary(2007)andaGenomeTechnologyYoungInvesti- gatorAward(2009).SheservesasanadhocreviewerfortheNIHGCAT ScientificGrantReviewPanelandisanassociateeditorofBMCGenomics andformerlyGenomeResearch. ix
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