Computational molecular biology: an introduction
Saved in:
| Main Authors: | , |
|---|---|
| Format: | Book |
| Language: | English |
| Published: |
Chichester [u.a.]
Wiley
2005
|
| Edition: | Reprint. |
| Series: | Wiley series in mathematical and computational biology
|
| Subjects: | |
| Online Access: | Inhaltsverzeichnis |
| Physical Description: | IX, 286 S. Ill., graph. Darst. |
| ISBN: | 0471872512 0471872520 |
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Record in the Search Index
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| adam_text | COMPUTATIONAL MOLECULAR BIOLOGY AN INTRODUCTION PETER CLOTE DEPARTMENT
OF COMPUTER SCIENCE AND DEPARTMENT OF BIOLOGY, BOSTON COLLEGE, USA
FORMERLY LUDWIG-MAXIMILIANS-UNIVERSITDT MUNCHEN, GERMANY ROLFBACKOFEN
LUDWIG-MAXIMILIANS-UNIVERSITDT MUNCHEN, GERMANY JOHN WILEY & SONS, LTD
CHICHESTER * NEW YORK * WEINHEIM * BRISBANE * SINGAPORE * TORONTO
CONTENTS SERIES PREFACE XI PREFACE XIII 1 MOLECULAR BIOLOGY 1 1.1 SOME
ORGANIC CHEMISTRY 3 1.2 SMALL MOLECULES 4 1.3 SUGARS 6 1.4 NUCLEIC ACIDS
6 1.4.1 NUCLEOTIDES 6 1.4.2 DNA 8 1.4.3 RNA 13 1.5 PROTEINS 14 1.5.1
AMINO ACIDS 14 1.5.2 PROTEIN STRUCTURE 15 1.6 FROM DNA TO PROTEINS 17
1.6.1 AMINO ACIDS AND PROTEINS 17 1.6.2 TRANSCRIPTION AND TRANSLATION 19
1.7 EXERCISES 21 ACKNOWLEDGEMENTS AND REFERENCES 22 2 MATH PRIMER 23 2.1
PROBABILITY 23 2.1.1 RANDOM VARIABLES 25 2.1.2 SOME IMPORTANT
PROBABILITY DISTRIBUTIONS 27 2.1.3 MARKOV CHAINS 38 2.1.4
METROPOLIS-HASTINGS ALGORITHM 43 2.1.5 MARKOV RANDOM FIELDS AND GIBBS
SAMPLER 47 2.1.6 MAXIMUM LIKELIHOOD 52 2.2 COMBINATORIAL OPTIMIZATION 53
2.2.1 LAGRANGE MULTIPLIERS 53 2.2.2 GRADIENT DESCENT 54 2.2.3 HEURISTICS
RELATED TO SIMULATED ANNEALING 54 2.2.4 APPLICATIONS OF MONTE CARLO 55
2.2.5 GENETIC ALGORITHMS 60 2.3 ENTROPY AND APPLICATIONS TO MOLECULAR
BIOLOGY 61 2.3.1 INFORMATION THEORETIC ENTROPY 62 2.3.2 SHANNON IMPLIES
BOLTZMANN 63 VIII CONTENTS 2.3.3 SIMPLE STATISTICAL GENOMIC ANALYSIS 66
2.3.4 GENOMIC SEGMENTATION ALGORITHM 69 2.4 EXERCISES 72 2.5 APPENDIX:
MODIFICATION OF BEZOUT S LEMMA 77 ACKNOWLEDGEMENTS AND REFERENCES 79 3
SEQUENCE ALIGNMENT 81 3.1 MOTIVATING EXAMPLE 83 3.2 SCORING MATRICES 84
3.3 GLOBAL PAIRWISE SEQUENCE ALIGNMENT 88 3.3.1 DISTANCE METHODS 88
3.3.2 ALIGNMENT WITH TANDEM DUPLICATION 99 3.3.3 SIMILARITY METHODS 110
3.4 MULTIPLE SEQUENCE ALIGNMENT ILL 3.4.1 DYNAMIC PROGRAMMING 112 3.4.2
GIBBS SAMPLER 112 3.4.3 MAXIMUM-WEIGHT TRACE 114 3.4.4 HIDDEN MARKOV
MODELS 117 3.4.5 STEINER SEQUENCES 117 3.5 GENOMIC REARRANGEMENTS * * *
H8 3.6 LOCATING CRYPTOGENES AND GUIDE RNA 120 3.6.1 ANCHOR AND
PERIODICITY RULES 122 3.6.2 SEARCH FOR CRYPTOGENES 122 3.7 EXPECTED
LENGTH OF GRNA IN TRYPANOSOMES 123 3.8 EXERCISES 128 3.9 APPENDIX:
MAXIMUM-LIKELIHOOD ESTIMATION FOR PAIR PROBABILITIES 132
ACKNOWLEDGEMENTS AND REFERENCES 133 4 ALL ABOUT EVE 13 5 4.1
INTRODUCTION 135 4.2 RATE OF EVOLUTIONARY CHANGE 137 4.2.1 AMINO ACID
SEQUENCES 137 4.2.2 NUCLEOTIDE SEQUENCES 139 4.3 CLUSTERING METHODS 144
4.3.1 ULTRAMETRIC TREES 147 4.3.2 ADDITIVE METRIC 152 4.3.3 ESTIMATING
BRANCH LENGTHS 156 4.4 MAXIMUM LIKELIHOOD 157 4.4.1 LIKELIHOOD OF A TREE
159 4.4.2 RECURSIVE DEFINITION FOR THE LIKELIHOOD 160 4.4.3 OPTIMAL
BRANCH LENGTHS FOR FIXED TOPOLOGY 162 4.4.4 DETERMINING THE TOPOLOGY 166
4.5 QUARTET PUZZLING 166 4.5.1 QUARTET PUZZLING STEP 169 4.5.2 MAJORITY
CONSENSUS TREE 170 4.6 EXERCISES * 171 CONTENTS IX ACKNOWLEDGEMENTS AND
REFERENCES 173 5 HIDDEN MARKOV MODELS 175 5.1 LIKELIHOOD AND SCORING A
MODEL 177 5.2 RE-ESTIMATION OF PARAMETERS 180 5.2.1 BAUM-WELCH METHOD
181 5.2.2 EM AND JUSTIFICATION OF THE BAUM-WELCH METHOD 184 5.2.3
BALDI-CHAUVIN GRADIENT DESCENT 187 5.2.4 MAMITSUKA S MA ALGORITHM 191
5.3 APPLICATIONS 193 5.3.1 MULTIPLE SEQUENCE ALIGNMENT 193 5.3.2 PROTEIN
MOTIFS 194 5.3.3 EUKARYOTIC DNA PROMOTOR REGIONS 195 5.4 EXERCISES 197
ACKNOWLEDGEMENTS AND REFERENCES 198 6 STRUCTURE PREDICTION 201 6.1 RNA
SECONDARY STRUCTURE 202 6.2 DNA STRAND SEPARATION 213 6.3 AMINO ACID
PAIR POTENTIALS 223 6.4 LATTICE MODELS OF PROTEINS 228 6.4.1 MONTE CARLO
AND THE HETEROPOLYMER PROTEIN MODEL 231 6.4.2 GENETIC ALGORITHM FOR
FOLDING IN THE HP MODEL 233 6.5 HART AND ISTRIAL S APPROXIMATION
ALGORITHM 234 6.5.1 PERFORMANCE 234 6.5.2 LOWER BOUND 236 6.5.3 BLOCK
STRUCTURE, FOLDING POINT, AND BALANCED CUT 239 6.6 CONSTRAINT-BASED
STRUCTURE PREDICTION 243 6.7 PROTEIN THREADING 246 6.7.1 DEFINITION 246
6.7.2 A BRANCH-AND-BOUND ALGORITHM 249 6.7.3 NP-HARDNESS 258 6.8
EXERCISES 259 ACKNOWLEDGEMENTS AND REFERENCES 261 APPENDIX A
MATHEMATICAL BACKGROUND 263 A. 1 ASYMPTOTIC COMPLEXITY 263 A.2 UNITS OF
MEASUREMENT 263 A.3 LAGRANGE MULTIPLIERS 264 APPENDIX B RESOURCES 265
B.I WEBSITES 265 B.2 THE PDB FORMAT 266 REFERENCES 269 INDEX 281
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| physical | IX, 286 S. Ill., graph. Darst. |
| publishDate | 2005 |
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| spelling | Clote, Peter Verfasser aut Computational molecular biology an introduction Peter Clote ; Rolf Backofen Reprint. Chichester [u.a.] Wiley 2005 IX, 286 S. Ill., graph. Darst. txt rdacontent n rdamedia nc rdacarrier Wiley series in mathematical and computational biology Genetik - Mathematisches Modell Molekularbiologie - Mathematisches Modell Mathematisches Modell (DE-588)4114528-8 gnd rswk-swf Molekularbiologie (DE-588)4039983-7 gnd rswk-swf Molekularbiologie (DE-588)4039983-7 s Mathematisches Modell (DE-588)4114528-8 s DE-604 Backofen, Rolf Verfasser aut GBV Datenaustausch application/pdf http://bvbr.bib-bvb.de:8991/F?func=service&doc_library=BVB01&local_base=BVB01&doc_number=013057984&sequence=000001&line_number=0001&func_code=DB_RECORDS&service_type=MEDIA Inhaltsverzeichnis |
| spellingShingle | Clote, Peter Backofen, Rolf Computational molecular biology an introduction Genetik - Mathematisches Modell Molekularbiologie - Mathematisches Modell Mathematisches Modell (DE-588)4114528-8 gnd Molekularbiologie (DE-588)4039983-7 gnd |
| subject_GND | (DE-588)4114528-8 (DE-588)4039983-7 |
| title | Computational molecular biology an introduction |
| title_auth | Computational molecular biology an introduction |
| title_exact_search | Computational molecular biology an introduction |
| title_full | Computational molecular biology an introduction Peter Clote ; Rolf Backofen |
| title_fullStr | Computational molecular biology an introduction Peter Clote ; Rolf Backofen |
| title_full_unstemmed | Computational molecular biology an introduction Peter Clote ; Rolf Backofen |
| title_short | Computational molecular biology |
| title_sort | computational molecular biology an introduction |
| title_sub | an introduction |
| topic | Genetik - Mathematisches Modell Molekularbiologie - Mathematisches Modell Mathematisches Modell (DE-588)4114528-8 gnd Molekularbiologie (DE-588)4039983-7 gnd |
| topic_facet | Genetik - Mathematisches Modell Molekularbiologie - Mathematisches Modell Mathematisches Modell Molekularbiologie |
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