Welcome! Thankyouforjoiningus! Asyouexplorethisbook,youwillfindanumberofactive learningcomponentsthathelpyoulearnthematerialatyourownpace. 1. CODE CHALLENGES ask you to implement the algorithms that you will en- counter (in any programming language you like). These code challenges are hosted in the “Bioinformatics Textbook Track” location on Rosalind (http:// rosalind.info),awebsitethatwillautomaticallytestyourimplementations. 2. CHARGINGSTATIONSprovideadditionalinsightsonimplementingthealgo- rithmsyouencounter. However, wesuggesttryingtosolveaCodeChallenge beforeyouvisitaChargingStation. 3. EXERCISEBREAKSoffer“justintime”assessmentstestingyourunderstanding ofatopicbeforemovingtothenextone. 4. STOPandThinkquestionsinviteyoutoslowdownandcontemplatethecurrent materialbeforecontinuingtothenexttopic. 5. DETOURSprovideextracontentthatdidn’tquitefitinthemaintext. DDEETTOOUURR 6. FINALCHALLENGESaskyoutoapplywhatyouhavelearnedtorealexperi- mentaldatasets. This textbook powers our popular online courses on Coursera. We encourage you to sign up for a session and learn this material while interacting with thousands of othertalentedstudentsfromaroundtheworld. Youcanalsofindlecturevideosand PowerPointslidesatthetextbookwebsite,http://bioinformaticsalgorithms.org. i Bioinformatics Algorithms: An Active Learning Approach 2nd Edition, Vol. I Phillip Compeau & Pavel Pevzner http://bioinformaticsalgorithms.org © 2015 Copyright©2015byPhillipCompeauandPavelPevzner. Allrightsreserved. Thisbookoranyportionthereofmaynotbereproducedorusedinanymannerwhatso- everwithouttheexpresswrittenpermissionofthepublisherexceptfortheuseofbrief quotationsinabookreview. PrintedintheUnitedStatesofAmerica FirstPrinting,2015 ISBN:978-0-9903746-1-9 LibraryofCongressControlNumber: 2015945208 ActiveLearningPublishers,LLC 9768ClaiborneSquare LaJolla,CA92037 Tomyfamily. —P.C. Tomyparents. —P.P. Volume I Overview CHAPTER1—p.2 CHAPTER2—p.66 vi CHAPTER3—p.115 CHAPTER4—p.182 CHAPTER5—p.222 CHAPTER6—p.292 vii What To Expect in Volume II... CHAPTER7 CHAPTER8 viii CHAPTER9 CHAPTER10 CHAPTER11 ix