计算分子生物学导论

　　Ever since the structure of DNA was unraveled in 1953， molecular biology has witnessed tremendous advances. With the increase in our ability to manipulate biomolecular sequences， a huge amount of data has been and is being generated. The need to process the information that is pouring from laboratories all over the world， so that it can be of use to further scientific advance， has created entirely new problems that are interdisciplinary in nature. Scientists from the biological sciences are the creators and ultimate users of this data. However， due to sheer size and complexity， between creation and use the help of many other diisciplines is required， in particular those from the mathematical and computing sciences. This need has created a new field， which goes by the general name of computational molecular biology....

暂缺《计算分子生物学导论》作者简介

Preface.
BookOverview
Exercises
Errors
Acknowledgments
1BasicConceptsofMolecularBiology
1.1Life
1.2Proteins
1.3NucleicAcids
1.3.1DNA
1.3.2RNA
1.4TheMechanismsofMolecularGenetics
1.4.1GenesandtheGeneticCode
1.4.2Transcription,Translation,andProteinSynthesis
1.4.3JunkDNAandReadingFrames
1.4.4Chromosomes
1.4.5IstheGenomelikeaComputerProgram?
1.5HowtheGenomeIsStudied
1.5.1MapsandSequences
1.5.2SpecificTechniques
1.6TheHumanGenomeProject
1.7SequenceDatabases
Exercises
BibliographicNotes
2Strings,Graphs,andAlgorithms
2.1Strings
2.2Graphs
2.3Algorithms
Exercises
BibliographicNotes
3SequenceComparisonandDatabaseSearch
3.1BiologicalBackground
3.2ComparingTwoSequences
3.2.1GlobalComparison—TheBasicAlgorithm
3.2.2LocalComparison
3.2.3SemiglobalComparison
3.3ExtensionstotheBasicAlgorithms
3.3.1SavingSpace
3.3.2GeneralGapPenaltyFunctions
3.3.3AffineGapPenaltyFunctions
3.3.4ComparingSimilarSequences
3.4ComparingMultipleSequences
3.4.1TheSPMeasure
3.4.2StarAlignments
3.4.3TreeAlignments
3.5DatabaseSearch
3.5.1PAMMatrices
3.5.2BLAST
3.5.3FAST
3.6OtherIssues
*3.6.1SimilarityandDistance
3.6.2ParameterChoiceinSequenceComparison
3.6.3StringMatchingandExactSequenceComparison
Summary
Exercises
BibliographicNotes
4FragmentAssemblyofDNA
4.1BiologicalBackground
4.1.1TheIdealCase
4.1.2Complications
4.1.3AlternativeMethodsforDNASequencing
4.2Models
4.2.1ShortestCommonSuperstring
4.2.2Reconstruction
4.2.3Multicontig
*4.3Algorithms
4.3.1RepresentingOverlaps
4.3.2PathsOriginatingSuperstrings
4.3.3ShortestSuperstringsasPaths
4.3.4TheGreedyAlgorithm
4.3.5AcyclicSubgraphs
4.4Heuristics
4.4.1FindingOverlaps
Exercises
BibliographicNotes
5PhysicalMappingofDNA
5.1BiologicalBackground
5.1.1RestrictionSiteMapping
5.1.2HybridizationMapping
5.2Models
5.2.1RestrictionSiteModels
5.2.2IntervalGraphModels
5.2.3TheConsecutiveOnesProperty
5.2.4AlgorithmicImplications
5.3AnAlgorithmfortheC1PProblem
5.4AnApproximationforHybridizationMappingwithErrors
5.4.1AGraphModel
5.4.2AGuarantee
5.4.3ComputationalPractice
5.5HeuristicsforHybridizationMapping
5.5.1ScreeningChimericClones
5.5.2ObtainingaGoodProbeOrdering
Summary
Exercises
BibliographicNotes
6PhylogeneticTrees
6.1CharacterStatesandthePerfectPhylogenyProblem
6.2BinaryCharacterStates
6.3TwoCharacters
6.4ParsimonyandCompatibilityinPhylogenies
6.5AlgorithmsforDistanceMatrices
6.5.1ReconstructingAdditiveTrees
*6.5.2ReconstructingU!trametricTrees
6.6AgreementBetweenPhylogenies
Summary
Exercises
BibliographicNotes
7GenomeRearrangements
7.1BiologicalBackground
7.2OrientedBlocks
7.2.1Definitions
7.2.2Breakpoints
7.2.3TheDiagramofRealityandDesire
7.2.4InterleavingGraph
7.2.5BadComponents
7.2.6Algorithm
7.3UnorientedBlocks
7.3.1Strips
7.3.2Algorithm
Summary
Exercises
BibliographicNotes
8MolecularStructurePrediction
8.1RNASecondaryStructurePrediction
8.2TheProteinFoldingProblem
8.3ProteinThreading
Summary
Exercises
BibliographicNotes
9Epilogue:ComputingwithDNA
9.1TheHamiltonianPathProblem
9.2Satisfiability
9.3ProblemsandPromises
Exercises
BibliographicNotesandFurtherSources
AnswerstoSelectedExercises
References
Index...