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Computational Biology Jeremy Ramsden Bioinformatics An Introduction Third Edition Computational Biology Volume 21 Editors-in-Chief Andreas Dress CAS-MPG PartnerInstitute for Computational Biology,Shanghai, China Michal Linial HebrewUniversity of Jerusalem,Jerusalem, Israel OlgaTroyanskaya Princeton University, Princeton, NJ, USA Martin Vingron MaxPlanckInstitute for Molecular Genetics, Berlin,Germany Editorial Board RobertGiegerich, University of Bielefeld,Bielefeld, Germany Janet Kelso, MaxPlanckInstitute for Evolutionary Anthropology, Leipzig, Germany Gene Myers,MaxPlanck Institute of Molecular Cell Biology andGenetics, Dresden, Germany PavelA.Pevzner,University ofCalifornia, SanDiego, CA, USA Advisory Board Gordon Crippen, University of Michigan,Ann Arbor,MI,USA Joe Felsenstein,University of Washington,Seattle, WA,USA Dan Gusfield,University of California, Davis, CA,USA Sorin Istrail, Brown University, Providence,RI, USA ThomasLengauer, MaxPlanckInstitute forComputer Science, Saarbrücken, Germany Marcella McClure, MontanaState University, Bozeman,MO, USA Martin Nowak, HarvardUniversity, Cambridge, MA, USA DavidSankoff, University of Ottawa,Ottawa, ON,Canada RonShamir, TelAvivUniversity, TelAviv, Israel Mike Steel,University ofCanterbury, Christchurch, NewZealand Gary Stormo,Washington University in St.Louis, St.Louis, MO, USA Simon Tavaré,University ofCambridge, Cambridge, UK Tandy Warnow,University of Texas,Austin, TX,USA LonnieWelch, OhioUniversity, Athens, OH, USA The Computational Biology series publishes the very latest, high-quality research devotedtospecificissuesincomputer-assistedanalysisofbiologicaldata.Themain emphasis is on current scientific developments and innovative techniques in computational biology (bioinformatics), bringing to light methods from mathemat- ics, statistics and computer science that directly address biological problems currently under investigation. The series offers publications that present the state-of-the-art regarding the problemsinquestion;showcomputationalbiology/bioinformaticsmethodsatwork; and finally discuss anticipated demands regarding developments in future methodology. Titles can range from focused monographs, to undergraduate and graduate textbooks, and professional text/reference works. More information about this series at http://www.springer.com/series/5769 Jeremy Ramsden Bioinformatics An Introduction Third Edition 123 Jeremy Ramsden TheUniversity of Buckingham Buckingham UK ISSN 1568-2684 Computational Biology ISBN978-1-4471-6701-3 ISBN978-1-4471-6702-0 (eBook) DOI 10.1007/978-1-4471-6702-0 LibraryofCongressControlNumber:2015937382 SpringerLondonHeidelbergNewYorkDordrecht ©Springer-VerlagLondon2015 1stedition:©KluwerAcademicPublishers2004 2ndedition:©Springer-VerlagLondon2009 Thisworkissubjecttocopyright.AllrightsarereservedbythePublisher,whetherthewholeorpart of the material is concerned, specifically the rights of translation, reprinting, reuse of illustrations, recitation, broadcasting, reproduction on microfilms or in any other physical way, and transmission orinformationstorageandretrieval,electronicadaptation,computersoftware,orbysimilarordissimilar methodologynowknownorhereafterdeveloped. The use of general descriptive names, registered names, trademarks, service marks, etc. in this publicationdoesnotimply,evenintheabsenceofaspecificstatement,thatsuchnamesareexemptfrom therelevantprotectivelawsandregulationsandthereforefreeforgeneraluse. The publisher, the authors and the editors are safe to assume that the advice and information in this book are believed to be true and accurate at the date of publication. Neither the publisher nor the authorsortheeditorsgiveawarranty,expressorimplied,withrespecttothematerialcontainedhereinor foranyerrorsoromissionsthatmayhavebeenmade. Printedonacid-freepaper Springer-VerlagLondonLtd.ispartofSpringerScience+BusinessMedia(www.springer.com) Mi a tudvágyat szakhoz nem kötők, Átpillantását vágyuk az egésznek Imre Madách Preface to the Third Edition The publication of this third edition has provided the opportunity to carefully scrutinize the entire contents and update them wherever necessary. Overview and aims,organization andfeatures, andtargetaudiences remainunchanged.The main additionsareinPartIII(Applications),whichhasacquirednewsectionsorchapters on the seemingly ever-expanding “omics”—now metagenomics, toxicogenomics, glycomics,lipidomics,microbiomics,andphenomicsareallcovered,albeitmostly briefly. The increasing involvement of information theory with ecosystems man- agement,whichisundoubtedlyapartofbiology,wasfelttowarrantanewchapter onthattopic.Thenervoussystemhasalsobeenexplicitlyincluded:itisindubitably an information processor and at the same time biological and, therefore, certainly warrants inclusion, although consideration of the vastness of the topic and its extensive coverage elsewhere has kept the corresponding chapter brief. A section on the automation of biological research now concludes the work. In his contribution, entitled “The domain of information theory in biology,” to the 1956 Symposium on Information Theory in Biology,1 Henry Quastler remarks (p.188)that“everykindofstructureandeverykindofprocesshasitsinformational aspect and can be associated with information functions. In this sense, the domain of information theory is universal—that is, information analysis can be applied to absolutely anything.” This sentiment continues to pervade the present work. The author takes this opportunity to thank all those who kindly commented on the second edition. January 2015 1Yockey. vii Preface to the Second Edition Overview and Aims Thisbookisintendedasaself-containedguidetotheentirefieldofbioinformatics, interpreted as the application of information science to biology. There is a strong underlying belief that information is a profound concept underlying biology, and familiarity with the concepts of information should make it possible to gain many important new insights into biology. In other words, the vision underpinning this book goes beyond the narrow interpretation of bioinformatics sometimes encoun- tered,whichmayconfineitselftospecifictaskssuchastheattemptedidentification of genes in a DNA sequence. Organization and Features The chapters are grouped into three parts, respectively covering the relevant fundamentals of information science, overviewing all of biology, and surveying applications.ThusPartI(Fundamentals)carefullyexplainswhatinformationis,and discusses attributes such as value and quality, and its multiple meanings of accu- racy, meaning, and effect. The transmission of information through channels is described.Briefsummariesofthenecessaryelements ofset theory,combinatorics, probability,likelihood,clustering,andpatternrecognitionaregiven.Conceptssuch asrandomness,complexity,systems,andnetworks,neededfortheunderstandingof biologicalorganization,arealsodiscussed.PartII(Biology)coversbothorganismal (ontogeny and phylogeny, as well as genome structure) and molecular aspects. Part III (Applications) is devoted to the most important practical applications of bioinformatics, notably gene identification, transcriptomics, proteomics, interacto- mics (dealing with networks of interactions), and metabolomics. These chapters startwithadiscussionoftheexperimentalaspects(suchasDNAsequencinginthe genomicschapter),andthenmoveontoathoroughdiscussionofhowthedataare analysed. Specifically, medical applications are grouped in a separate chapter. ix x PrefacetotheSecondEdition Anumberofproblemsaresuggested,manyofwhichareopen-endedandintended to stimulate further thinking. The bibliography points to specialized monographs andreviewarticlesexpandingonmaterialinthetext,andincludesguidereferences to very recently reported research not yet to be found in reviews. Target Audiences Thisbookisprimarilyintendedasatextbookforundergraduates,forwhomitaims tobe acomplete study companion. As such,it will also be useful tothebeginning graduate student. A secondary audience is physical scientists seeking a comprehensive but suc- cinct guide to biology, and biological scientists wishing to better acquaint them- selves with some of the physicochemical and mathematical aspects that underpin the applications. Itishopedthatallreaders willfindthatevenfamiliarmaterial ispresentedwith fresh insight, and will be inspired to new thoughts. The author takes this opportunity to thank all those who gave him their com- ments on the first edition. May 2008 Preface to the First Edition Thislittle bookattemptstogiveaself-contained account ofbioinformatics, sothat the newcomer to the field may, whatever his point of departure, gain a rather complete overview. At the same timeit makes no claimto be comprehensive: The fieldisalreadytoovast—andletitberememberedthatalthoughitsrecognitionasa distinct discipline (i.e., one after which departments and university chairs are named) is recent, its roots go back a long time. Given that many of the newcomers arrive from either biology or informatics, it wasanobviousconsideration thatfor thebooktoachieveitsaimofcompleteness, large portions would have to deal with matter already known to those with back- groundsineitherofthosetwofields;thatis,intheparticularchaptersdealingwith them, the book would provide no information for them. Since such chapters could hardlybeomitted,Ihavetriedtoconsidersuchmatterinthelightofbioinformatics asawhole,sothateventhestudentostensiblyfamiliarwithitcouldbenefitfroma fresh viewpoint. In one regard especially, this book cannot be comprehensive. The field is developingextraordinarilyrapidlyanditwouldhavebeenartificialandarbitraryto takeasnapshotofthedetailsofcontemporaryresearch.HenceIhavetriedtofocus on a thorough grounding of concepts, which will enable the student not only to understandcontemporaryworkbutshouldalsoserveasaspringboardforhisorher owndiscoveries.Muchoftherawmaterialofbioinformaticsisopenandaccessible toallviatheInternet,powerfulcomputingfacilitiesareubiquitous,andwemaybe confident thatvast tracts ofthefieldlie yetuncultivated.Thisaccessibility extends to the literature: Research papers on any topic can usually be found rapidly by an Internet search and, therefore, I have not aimed at providing a comprehensive bibliography. Inbioinformatics,so much is tobe done,the raw material to hand isalready so vastandvastlyincreasing,andtheproblemstobesolvedaresoimportant(perhaps the most important of any science at present), we may be entering an era compa- rable to the great flowering of quantum mechanics in the first three decades of the twentiethcentury,duringwhichtherewereperiodswhenpracticallyeverydoctoral thesiswasamajorbreakthrough.Ifthisbookisabletoinspirethestudenttotakeup some of the challenges, then it will have accomplished a large part of what it sets out to do. xi