Andrzej K. Konopka, M. James C. Crabbe0824709829, 9780824709822, 9780203021415
Compact Handbook of Computational Biology provides detailed coverage of
• pragmatic analysis of nucleic acid and protein sequences and structures • definition and detection of motifs in nucleic acid and protein sequences • protein structure prediction • discrete models of biopolymers • computer-assisted research on protein folding • computer-assisted studies of DNA–protein interactions • computer-assisted genomics, proteomics and comparative genomics • computer-assisted studies of genome evolution at the molecular (DNA) level
The handbook is designed as a reliable, integrated reference for specialists, as well as an instructional manual for students and trainees in computational biology, bioinformatics, proteomics, molecular genetics (sometimes referred to as functional genomics), and related fields. It can also serve as a practical resource for industrial executives in charge of bioinformatics, genomics, and proteomics, as well as for science administrators in universities and scientific foundations. Lawyers, journalists, historians of science, forensic scientists, and medical professionals can also find this text useful as a desk reference and as a guide to the literature.
Table of contents :
Cover Page……Page 1
Title: Compact Handbook of Computational Biology……Page 2
ISBN 0824709829……Page 3
Foreword……Page 4
Contents……Page 6
Contributors……Page 8
Chapter 1: Introduction: Computational Biology in 14 Brief Paragraphs……Page 10
⸀ 䤀一吀刀伀䐀唀䌀吀䤀伀一……Page 16
2. LEADING METAPHORS AND CONCEPTS BEHIND SEQUENCE ANALYSIS……Page 18
2.1. Sequence Hypothesis and the Central Dogma as Inspirations for Sequence Analysis……Page 20
2.2. A Paradigm of Biomolecular Cryptology: Its Strengths and Limitations……Page 22
㈀⸀㈀⸀⸀ 䄀氀瀀栀愀戀攀琀猀……Page 23
2.2.2. Metaphor of Functional Codes is Too Esoteric to be Practical……Page 24
2.2.3. Classification Codes and Functionally Equivalent Sequences……Page 25
㌀⸀⸀ 䌀漀洀瀀甀琀愀琀椀漀渀愀氀 䈀椀漀氀漀最礀 瘀猀⸀ 䈀椀漀椀渀昀漀爀洀愀琀椀挀猀……Page 26
㌀⸀㈀⸀ 一甀挀氀攀椀挀 䄀挀椀搀 瘀猀⸀ 倀爀漀琀攀椀渀 匀攀焀甀攀渀挀攀 䄀渀愀氀礀猀椀猀……Page 28
3.3. Sequence Annotation “By Signal” vs. Annotation “By Content”……Page 29
㌀⸀㐀⸀ 匀攀琀 漀昀 䴀愀渀礀 匀攀焀甀攀渀挀攀猀 瘀猀⸀ 匀椀渀最氀攀ⴀ匀攀焀甀攀渀挀攀 䄀渀愀氀礀猀椀猀……Page 30
㐀⸀⸀ 匀礀渀琀愀砀ⴀ䜀攀渀攀爀愀琀椀渀最 ⠀䜀攀渀攀爀愀琀椀瘀攀⤀ 䴀漀搀攀氀猀 漀昀 䰀愀渀最甀愀最攀……Page 31
㐀⸀㈀⸀ 匀琀愀琀椀猀琀椀挀愀氀 䴀漀搀攀氀猀 漀昀 倀爀椀渀琀攀搀 吀攀砀琀猀……Page 34
4.2.1. Discrete Uniform Distribution of Letter Frequencies and Bernoulli Text……Page 38
㔀⸀ 倀刀䄀䜀䴀䄀吀䤀䌀 䤀一䘀䔀刀䔀一䌀䔀……Page 41
6.1. Overlapping and Nonoverlapping Counts of k-Gram Frequencies……Page 45
6.2. Some Statistical Practices of Particular Importance in Sequence Analysis……Page 47
刀䔀䘀䔀刀䔀一䌀䔀匀……Page 49
⸀ 䴀伀吀䤀䘀匀 䤀一 匀䔀儀唀䔀一䌀䔀匀……Page 56
㈀⸀㈀⸀ 䤀搀攀渀琀椀琀礀……Page 59
㈀⸀㌀⸀ 一漀渀琀爀愀渀猀椀琀椀瘀攀 刀攀氀愀琀椀漀渀……Page 60
㈀⸀㐀⸀⸀ 䤀渀琀爀漀搀甀挀椀渀最 琀栀攀 䤀搀攀愀 漀昀 愀 䴀漀搀攀氀……Page 61
2.4.2. Expanding on the Idea of Models—Two more Possible Definitions of Similarity……Page 63
㌀⸀⸀ 匀攀愀爀挀栀椀渀最 昀漀爀 愀 䘀椀砀攀搀 䴀漀琀椀昀……Page 66
㌀⸀⸀⸀ 倀爀愀挀琀椀挀愀氀氀礀 䘀愀猀琀 匀攀愀爀挀栀攀猀……Page 68
㌀⸀㈀⸀ 䄀瀀瀀爀漀砀椀洀愀琀攀 䴀愀琀挀栀椀渀最猀……Page 70
㌀⸀㈀⸀⸀ 匀琀爀椀渀最 匀攀愀爀挀栀椀渀最 眀椀琀栀 䐀椀昀昀攀爀攀渀挀攀猀……Page 71
㌀⸀㌀⸀⸀ 䌀漀洀瀀愀挀琀椀漀渀……Page 73
㌀⸀㌀⸀㌀⸀ 䔀昀昀椀挀椀攀渀琀 䌀漀渀猀琀爀甀挀琀椀漀渀猀……Page 75
㌀⸀㌀⸀㐀⸀ 䔀昀昀椀挀椀攀渀琀 匀琀漀爀愀最攀……Page 76
㌀⸀㐀⸀ 匀琀爀甀挀琀甀爀愀氀 䴀漀琀椀昀猀……Page 78
㐀⸀⸀⸀ 䜀攀渀攀爀愀氀 䄀氀最漀爀椀琀栀洀猀……Page 80
4.1.2. A Powerful Algorithm for Identifying Dispersed Exact Repeats—KMR……Page 81
㐀⸀㈀⸀⸀ 䴀漀搀攀氀 昀漀爀 吀愀渀搀攀洀 䄀爀爀愀礀猀 ⠀匀愀琀攀氀氀椀琀攀猀⤀……Page 83
㐀⸀㈀⸀㈀⸀ 䈀甀椀氀搀椀渀最 倀爀攀昀椀砀 匀愀琀攀氀氀椀琀攀 䴀漀搀攀氀猀……Page 86
㐀⸀㈀⸀㌀⸀ 䌀漀渀猀攀渀猀甀猀 匀愀琀攀氀氀椀琀攀 䴀漀搀攀氀猀……Page 88
㔀⸀⸀ 匀瀀攀氀氀椀渀最 匀椀洀瀀氀攀 䴀漀搀攀氀猀……Page 90
㔀⸀㈀⸀⸀ 䤀渀琀爀漀搀甀挀椀渀最 匀琀爀甀挀琀甀爀攀搀 䴀漀搀攀氀猀……Page 91
㔀⸀㈀⸀㈀⸀ 匀琀愀琀攀洀攀渀琀 漀昀 琀栀攀 匀琀爀甀挀琀甀爀攀搀 䴀漀搀攀氀 倀爀漀戀氀攀洀……Page 92
5.2.3. Algorithms for the Special Case of a Known Interval of Distance……Page 94
5.2.4. Extending the Algorithms to Extract Structured Models Having p>2 Parts……Page 100
刀䔀䘀䔀刀䔀一䌀䔀匀……Page 102
⸀⸀ 倀愀椀爀眀椀猀攀 䌀漀洀瀀愀爀椀猀漀渀……Page 108
⸀⸀⸀ 䐀漀琀 䴀愀琀爀椀砀 䄀渀愀氀礀猀椀猀……Page 109
⸀⸀㈀⸀ 䐀礀渀愀洀椀挀 倀爀漀最爀愀洀洀椀渀最 䴀攀琀栀漀搀猀……Page 110
⸀㈀⸀ 䴀甀氀琀椀瀀氀攀 䄀氀椀最渀洀攀渀琀……Page 114
⸀㈀⸀⸀ 䜀氀漀戀愀氀 䴀甀氀琀椀瀀氀攀 䄀氀椀最渀洀攀渀琀 䴀攀琀栀漀搀猀……Page 115
⸀㈀⸀㈀⸀ 䰀漀挀愀氀 䴀甀氀琀椀瀀氀攀 䄀氀椀最渀洀攀渀琀 䴀攀琀栀漀搀猀……Page 123
1.2.3. Iterative Multiple Alignment Optimization and Alternative Techniques……Page 124
1.2.4 Evaluation of Multiple Alignment Methods……Page 128
⸀㌀⸀ 匀挀漀爀椀渀最 䄀洀椀渀漀 䄀挀椀搀 匀甀戀猀琀椀琀甀琀椀漀渀猀……Page 129
⸀㐀⸀ 匀攀焀甀攀渀挀攀 倀愀琀琀攀爀渀猀……Page 132
⸀㐀⸀⸀ 䌀氀愀猀猀椀昀礀椀渀最 匀攀焀甀攀渀挀攀 䴀漀琀椀昀猀……Page 133
⸀㐀⸀㈀⸀ 匀攀焀甀攀渀挀攀 倀愀琀琀攀爀渀 䐀攀琀攀挀琀椀漀渀 䴀攀琀栀漀搀猀……Page 134
⸀㐀⸀㌀⸀ 䤀渀琀攀爀渀愀氀 匀攀焀甀攀渀挀攀 刀攀瀀攀愀琀 䐀攀琀攀挀琀椀漀渀……Page 139
⸀㔀⸀⸀ 䴀漀搀攀猀 昀漀爀 䌀愀氀挀甀氀愀琀椀渀最 倀爀漀昀椀氀攀猀……Page 142
⸀㔀⸀㈀⸀ 倀爀漀昀椀氀攀 匀攀愀爀挀栀 䴀攀琀栀漀搀猀……Page 145
⸀㔀⸀㌀⸀ 匀攀焀甀攀渀挀攀 圀攀椀最栀琀椀渀最……Page 146
⸀㔀⸀㐀⸀ 䠀䴀䴀ⴀ䈀愀猀攀搀 倀爀漀昀椀氀攀 匀攀愀爀挀栀椀渀最……Page 148
⸀㘀⸀⸀ 䘀䄀匀吀䄀……Page 149
⸀㘀⸀㈀⸀ 䈀䰀䄀匀吀……Page 150
⸀㘀⸀㌀⸀ 䘀愀猀琀 匀洀椀琀栀ᐠ圀愀琀攀爀洀愀渀 䰀漀挀愀氀 䄀氀椀最渀洀攀渀琀 匀攀愀爀挀栀攀猀……Page 153
2. PREDICTING SECONDARY STRUCTURAL FEATURES FROM PROTEIN SEQUENCES……Page 155
㈀⸀⸀ 倀爀漀瀀攀爀琀椀攀猀 漀昀 匀攀挀漀渀搀愀爀礀 匀琀爀甀挀琀甀爀攀……Page 156
㈀⸀㈀⸀ 䄀猀猀攀猀猀椀渀最 倀爀攀搀椀挀琀椀漀渀 䄀挀挀甀爀愀挀礀……Page 157
㈀⸀㌀⸀ 吀栀攀 䔀愀爀氀礀 倀爀攀搀椀挀琀椀漀渀 䴀攀琀栀漀搀猀……Page 160
㈀⸀㐀⸀ 䴀漀搀攀爀渀 䴀攀琀栀漀搀猀……Page 162
㈀⸀㐀⸀⸀ 一攀甀爀愀氀 一攀琀眀漀爀欀 䴀攀琀栀漀搀猀……Page 164
㈀⸀㐀⸀㈀⸀ 欀ⴀ一攀愀爀攀猀琀ⴀ一攀椀最栀戀漀爀 䴀攀琀栀漀搀猀……Page 165
㈀⸀㐀⸀㌀⸀ 䐀椀猀挀爀椀洀椀渀愀渀琀 䄀渀愀氀礀猀椀猀……Page 168
㈀⸀㐀⸀㔀⸀ 䔀砀瀀氀漀爀椀渀最 匀攀挀漀渀搀愀爀礀 匀琀爀甀挀琀甀爀攀ⴀ匀瀀攀挀椀昀椀挀 䄀洀椀渀漀 䄀挀椀搀 䔀砀挀栀愀渀最攀猀……Page 169
㈀⸀㔀⸀ 䌀漀渀猀攀渀猀甀猀 倀爀攀搀椀挀琀椀漀渀 愀渀搀 䄀氀椀最渀洀攀渀琀 儀甀愀氀椀琀礀……Page 170
㌀⸀ 倀刀䔀䐀䤀䌀吀䤀伀一 伀䘀 吀刀䄀一匀䴀䔀䴀䈀刀䄀一䔀 匀䔀䜀䴀䔀一吀匀……Page 173
3.1. Prediction of alpha-Helical TM Segments……Page 174
3.3. Prediction of beta-Strand Transmembrane Regions……Page 177
㐀⸀ 倀刀䔀䐀䤀䌀吀䤀伀一 伀䘀 倀刀伀吀䔀䤀一 䄀一吀䤀䜀䔀一䤀䌀 匀䤀吀䔀匀……Page 178
㔀⸀ 倀刀䔀䐀䤀䌀吀䤀一䜀 䌀伀䤀䰀䔀䐀ⴀ䌀伀䤀䰀 匀吀刀唀䌀吀唀刀䔀匀……Page 180
刀䔀䘀䔀刀䔀一䌀䔀匀……Page 181
⸀ 䤀一吀刀伀䐀唀䌀吀䤀伀一……Page 196
㈀⸀㈀⸀ 䌀漀渀琀愀挀琀 䜀爀愀瀀栀猀……Page 197
㌀⸀⸀⸀ 䔀渀甀洀攀爀愀琀椀漀渀……Page 201
㌀⸀⸀㌀⸀ 吀栀攀 刀一䄀 䘀漀氀搀椀渀最 倀爀漀戀氀攀洀……Page 204
㌀⸀㈀⸀⸀ 䔀渀甀洀攀爀愀琀椀漀渀……Page 207
㌀⸀㈀⸀㈀⸀ 䔀渀攀爀最礀 䘀甀渀挀琀椀漀渀猀……Page 208
㌀⸀㈀⸀㌀⸀ 吀栀攀 䰀愀琀琀椀挀攀 倀爀漀琀攀椀渀 䘀漀氀搀椀渀最 倀爀漀戀氀攀洀……Page 209
㐀⸀⸀ 吀栀攀 刀愀渀搀漀洀 䜀爀愀瀀栀 䴀漀搀攀氀……Page 210
㐀⸀㈀⸀ 倀爀攀搀椀挀琀椀漀渀猀……Page 211
㔀⸀⸀ 吀栀攀 倀爀漀搀甀挀琀 匀瀀愀挀攀 䴀漀搀攀氀……Page 212
㔀⸀㌀⸀⸀ 䔀砀栀愀甀猀琀椀瘀攀 䔀渀甀洀攀爀愀琀椀漀渀……Page 214
㔀⸀㌀⸀㈀⸀ 匀攀焀甀攀渀挀攀猀 漀昀 䌀栀愀椀渀 䰀攀渀最琀栀 渀㴀㘀……Page 215
㔀⸀㌀⸀㐀⸀ 匀琀愀琀椀猀琀椀挀愀氀 䔀瘀愀氀甀愀琀椀漀渀 漀昀 匀攀焀甀攀渀挀攀 匀瀀愀挀攀猀 眀椀琀栀 䌀栀愀椀渀 䰀攀渀最琀栀猀 渀㸀㌀ ……Page 220
㔀⸀㌀⸀㔀⸀ 匀栀愀瀀攀 匀瀀愀挀攀 吀漀瀀漀氀漀最礀……Page 222
㘀⸀ 䌀伀一䌀䰀唀匀䤀伀一匀 䄀一䐀 伀唀吀䰀伀伀䬀……Page 223
刀䔀䘀䔀刀䔀一䌀䔀匀……Page 224
⸀⸀ 吀栀攀 匀栀愀瀀攀猀 愀渀搀 匀椀稀攀猀 漀昀 倀爀漀琀攀椀渀猀……Page 232
⸀㌀⸀ 匀攀挀漀渀搀愀爀礀 匀琀爀甀挀琀甀爀攀……Page 233
⸀㐀⸀ 倀愀挀欀攀搀 䰀愀礀攀爀猀……Page 235
1.5. Barrel Structures and Beta-Helices……Page 236
⸀㘀⸀ 倀爀漀琀攀椀渀 吀漀瀀漀氀漀最礀……Page 237
⸀㜀⸀ 䐀漀洀愀椀渀 匀琀爀甀挀琀甀爀攀……Page 238
㈀⸀⸀ 䘀漀氀搀椀渀最 䤀渀 嘀椀琀爀漀 愀渀搀 䤀渀 嘀椀瘀漀……Page 239
㈀⸀㈀⸀ 吀栀攀漀爀攀琀椀挀愀氀 䴀漀搀攀氀猀 漀昀 䘀漀氀搀椀渀最……Page 241
㈀⸀㌀⸀ 䘀漀氀搀椀渀最 䤀渀 匀椀氀椀挀漀……Page 242
㌀⸀ 倀刀伀吀䔀䤀一 匀吀刀唀䌀吀唀刀䔀 倀刀䔀䐀䤀䌀吀䤀伀一……Page 243
㌀⸀⸀ 匀琀爀甀挀琀甀爀攀 倀爀攀昀攀爀攀渀挀攀 匀琀愀琀椀猀琀椀挀猀……Page 244
㌀⸀㈀⸀⸀ 匀攀焀甀攀渀挀攀 䄀氀椀最渀洀攀渀琀 愀渀搀 ㌀䐀ጠ䐀 䴀愀琀挀栀椀渀最……Page 245
㌀⸀㈀⸀㈀⸀ 䴀漀氀攀挀甀氀愀爀 䴀漀搀攀氀椀渀最 愀渀搀 吀栀爀攀愀搀椀渀最……Page 246
䄀䌀䬀一伀圀䰀䔀䐀䜀䴀䔀一吀匀……Page 247
刀䔀䘀䔀刀䔀一䌀䔀匀……Page 248
⸀ 䤀一吀刀伀䐀唀䌀吀䤀伀一……Page 250
㈀⸀ 匀䔀儀唀䔀一䌀䔀ⴀ䈀䄀匀䔀䐀 䴀䔀吀䠀伀䐀……Page 252
㌀⸀⸀ 䈀椀渀搀椀渀最 䘀爀攀攀 䔀渀攀爀最礀 䌀栀愀渀最攀 愀渀搀 匀瀀攀挀椀昀椀挀椀琀礀……Page 253
㌀⸀㈀⸀ 䄀瀀瀀氀椀挀愀琀椀漀渀 琀漀 琀栀攀 吀愀爀最攀琀 倀爀攀搀椀挀琀椀漀渀……Page 254
㐀⸀ 匀吀刀唀䌀吀唀刀䔀ⴀ䈀䄀匀䔀䐀 䴀䔀吀䠀伀䐀……Page 260
㐀⸀⸀ 䐀愀琀愀戀愀猀攀 䄀渀愀氀礀猀椀猀 愀渀搀 䐀攀爀椀瘀愀琀椀漀渀 漀昀 䌀漀渀琀愀挀琀 倀漀琀攀渀琀椀愀氀……Page 261
4.2. Sequence-Structure Threading……Page 263
㐀⸀㌀⸀⸀ 匀瀀攀挀椀昀椀挀椀琀礀 䐀椀昀昀攀爀攀渀挀攀 椀渀 䌀漀最渀愀琀攀 愀渀搀 一漀渀挀漀最渀愀琀攀 䈀椀渀搀椀渀最……Page 264
4.3.2 Specificity Difference in Symmetrical and Asymmetrical Binding……Page 268
㐀⸀㌀⸀㌀⸀ 䔀昀昀攀挀琀 漀昀 䌀漀漀瀀攀爀愀琀椀瘀椀琀礀 漀渀 䈀椀渀搀椀渀最 匀瀀攀挀椀昀椀挀椀琀礀……Page 269
㐀⸀㌀⸀㐀⸀ 䔀昀昀攀挀琀 漀昀 䐀一䄀 䐀攀昀漀爀洀愀琀椀漀渀……Page 270
㐀⸀㔀⸀ 倀爀漀琀攀椀渀 䐀攀猀椀最渀……Page 271
㐀⸀㘀⸀ 䌀漀渀琀爀椀戀甀琀椀漀渀 昀爀漀洀 䤀渀搀椀爀攀挀琀 刀攀愀搀漀甀琀 䴀攀挀栀愀渀椀猀洀……Page 274
㐀⸀㜀⸀ 䰀椀洀椀琀愀琀椀漀渀猀 愀渀搀 倀爀漀猀瀀攀挀琀猀……Page 275
㔀⸀⸀ 䌀漀渀昀漀爀洀愀琀椀漀渀愀氀 匀愀洀瀀氀椀渀最 愀渀搀 䔀渀攀爀最礀 䌀愀氀挀甀氀愀琀椀漀渀……Page 276
㔀⸀㌀⸀ 䰀椀洀椀琀愀琀椀漀渀猀 愀渀搀 倀爀漀猀瀀攀挀琀……Page 278
㘀⸀ 䄀倀倀䰀䤀䌀䄀吀䤀伀一 吀伀 䘀唀一䌀吀䤀伀一䄀䰀 䜀䔀一伀䴀䤀䌀匀……Page 280
䄀倀倀䔀一䐀䤀堀 ㈀㨀 䌀伀䴀倀唀吀䔀刀 倀刀伀䜀刀䄀䴀匀 䄀一䐀 䐀䄀吀䄀䈀䄀匀䔀匀……Page 283
刀䔀䘀䔀刀䔀一䌀䔀匀……Page 284
⸀ 䤀一吀刀伀䐀唀䌀吀䤀伀一……Page 288
㈀⸀⸀ 吀栀攀 㤀㜀 猀㨀 吀栀攀 䔀爀愀 漀昀 䌀漀渀猀攀渀猀甀猀 匀攀焀甀攀渀挀攀猀……Page 298
㈀⸀㈀⸀ 吀栀攀 㤀㠀 猀㨀 䔀砀瀀漀渀攀渀琀椀愀氀 䜀爀漀眀琀栀 愀渀搀 䤀渀挀爀攀愀猀椀渀最 匀瀀攀攀搀……Page 299
㈀⸀㈀⸀㈀⸀ 䠀漀眀 匀栀漀甀氀搀 匀攀焀甀攀渀挀攀 䐀愀琀愀 䈀攀 刀攀瀀爀攀猀攀渀琀攀搀㼀……Page 300
㈀⸀㌀⸀ 吀栀攀 䔀爀愀 漀昀 䜀攀渀漀洀攀 倀爀漀樀攀挀琀猀……Page 302
㌀⸀⸀⸀ 䐀一䄀……Page 304
㌀⸀㈀⸀⸀ 刀愀眀 匀攀焀甀攀渀挀攀猀……Page 306
㌀⸀㈀⸀㈀⸀ 䜀攀渀攀爀愀琀椀渀最 一攀眀 䐀攀猀挀爀椀瀀琀漀爀猀……Page 308
㌀⸀㈀⸀㌀⸀ 䰀攀愀爀渀椀渀最 匀椀最渀愀氀猀 昀漀爀 倀爀攀搀椀挀琀椀漀渀……Page 310
㌀⸀㈀⸀㐀⸀ 䠀椀搀搀攀渀 䴀愀爀欀漀瘀 䴀漀搀攀氀 愀渀搀 䜀攀渀攀爀愀氀椀稀愀琀椀漀渀……Page 312
㌀⸀㈀⸀㔀 䘀漀氀搀椀渀最 愀渀搀 匀椀洀甀氀愀琀椀漀渀……Page 313
㌀⸀㈀⸀㘀⸀ 䤀渀琀攀爀瀀爀攀琀椀渀最 一攀眀 䐀攀猀挀爀椀瀀琀漀爀猀 愀渀搀 䜀攀渀攀爀愀琀椀渀最 䴀漀搀攀氀猀……Page 314
㌀⸀㈀⸀㜀⸀ 伀瀀琀椀洀椀稀愀琀椀漀渀 愀渀搀 嘀愀氀椀搀愀琀椀漀渀……Page 316
㌀⸀㌀⸀⸀ 刀甀氀攀ⴀ䈀愀猀攀搀 愀渀搀 䬀渀漀眀氀攀搀最攀ⴀ䈀愀猀攀搀 匀礀猀琀攀洀猀……Page 319
㌀⸀㌀⸀㈀⸀ 一攀琀眀漀爀欀猀 愀渀搀 䜀爀愀瀀栀猀……Page 321
㌀⸀㐀⸀⸀ 䜀攀渀攀 䤀搀攀渀琀椀昀椀挀愀琀椀漀渀 椀渀 䔀甀欀愀爀礀漀琀椀挀 匀攀焀甀攀渀挀攀猀……Page 322
㌀⸀㐀⸀㈀⸀ 䐀愀琀愀 䴀椀渀椀渀最……Page 324
㌀⸀㐀⸀㌀⸀ 䌀漀洀瀀甀琀攀爀ⴀ匀椀洀甀氀愀琀攀搀 䘀甀渀挀琀椀漀渀猀……Page 327
㌀⸀㐀⸀㐀⸀ 䐀攀昀椀渀椀渀最 愀 䈀椀漀氀漀最椀挀愀氀 䌀漀渀琀攀砀琀……Page 331
㌀⸀㔀⸀㈀⸀ 倀爀漀琀攀椀渀 䔀砀瀀爀攀猀猀椀漀渀……Page 333
䄀䌀䬀一伀圀䰀䔀䐀䜀䴀䔀一吀匀……Page 336
䜀䰀伀匀匀䄀刀夀 伀䘀 吀䔀刀䴀匀……Page 337
刀䔀䘀䔀刀䔀一䌀䔀匀……Page 340
㈀⸀ 圀䠀䄀吀 䤀匀 䌀伀䴀倀䄀刀䄀吀䤀嘀䔀 䜀䔀一伀䴀䤀䌀匀㼀……Page 352
㌀⸀ 䔀嘀伀䰀唀吀䤀伀一䄀刀夀 䈀䄀匀䤀匀 伀䘀 䌀伀䴀倀䄀刀䄀吀䤀嘀䔀 䜀䔀一伀䴀䤀䌀匀……Page 353
㌀⸀⸀ 倀栀礀氀漀最攀渀攀琀椀挀 䄀瀀瀀爀漀愀挀栀 琀漀 䐀愀琀愀 匀攀氀攀挀琀椀漀渀……Page 355
㌀⸀㈀⸀⸀ 䌀漀洀瀀氀攀琀攀 䜀攀渀漀洀攀 䌀愀猀攀……Page 356
㌀⸀㌀⸀ 䰀愀爀最攀ⴀ匀挀愀氀攀 匀攀焀甀攀渀挀攀 䄀氀椀最渀洀攀渀琀……Page 357
㐀⸀⸀⸀ 䠀漀洀漀氀漀最漀甀猀 嘀攀爀琀攀戀爀愀琀攀 䜀攀渀攀猀 䐀愀琀愀戀愀猀攀 ⠀䠀伀嘀䔀刀䜀䔀一⤀……Page 360
4.1.2. Clusters of Orthologous Groups of Proteins……Page 365
㐀⸀㈀⸀ 䄀氀椀最渀洀攀渀琀 吀漀漀氀猀……Page 368
㐀⸀㌀⸀㈀⸀ 倀椀瀀䴀愀欀攀爀……Page 370
䄀倀倀䔀一䐀䤀堀……Page 374
刀䔀䘀䔀刀䔀一䌀䔀匀……Page 375
⸀ 䤀一吀刀伀䐀唀䌀吀䤀伀一……Page 378
㈀⸀ 伀刀䤀䜀䤀一 伀䘀 䴀䤀吀伀䌀䠀伀一䐀刀䤀䄀……Page 379
㌀⸀⸀ 唀渀椀瀀愀爀攀渀琀愀氀 椀渀栀攀爀椀琀愀渀挀攀……Page 380
㌀⸀㈀⸀ 刀攀挀漀洀戀椀渀愀琀椀漀渀……Page 383
㌀⸀㌀⸀ 匀椀稀攀 愀渀搀 匀栀愀瀀攀……Page 385
㌀⸀㐀⸀ 䜀攀渀攀琀椀挀 䌀漀搀攀……Page 392
㌀⸀㔀⸀ 刀一䄀 䔀搀椀琀椀渀最……Page 393
㐀⸀⸀ 䜀攀渀攀爀愀氀 倀爀漀瀀攀爀琀椀攀猀……Page 394
㐀⸀㈀⸀ 䜀攀渀漀洀攀 䘀攀愀琀甀爀攀猀 愀渀搀 伀爀最愀渀椀稀愀琀椀漀渀……Page 395
㐀⸀㌀⸀吀栀攀 一漀渀挀漀搀椀渀最 刀攀最椀漀渀猀……Page 402
㐀⸀㐀⸀ 䈀愀猀攀 䌀漀洀瀀漀猀椀琀椀漀渀……Page 408
㔀⸀⸀ 䜀攀渀漀洀攀 䘀攀愀琀甀爀攀猀 愀渀搀 伀爀最愀渀椀稀愀琀椀漀渀……Page 410
㔀⸀㈀⸀吀栀攀 䐀ⴀ䰀漀漀瀀 刀攀最椀漀渀……Page 411
㔀⸀㌀⸀ 䈀愀猀攀 䌀漀洀瀀漀猀椀琀椀漀渀 愀渀搀 匀欀攀眀……Page 415
㔀⸀㐀⸀ 䔀瘀漀氀甀琀椀漀渀愀爀礀 刀愀琀攀 漀昀 琀栀攀 䴀椀琀漀挀栀漀渀搀爀椀愀氀 䜀攀渀漀洀攀 椀渀 䴀愀洀洀愀氀猀……Page 421
㔀⸀㔀⸀ 刀愀琀攀 䠀攀琀攀爀漀最攀渀攀椀琀礀 漀昀 琀栀攀 䴀椀琀漀挀栀漀渀搀爀椀愀氀 䜀攀渀漀洀攀 椀渀 䴀愀洀洀愀氀猀……Page 425
6.1. Phylogenetic analysis based on the gene order differences of mitochondrial genomes……Page 427
6.2. Phylogenetic Inferences Based on the Evolutionary Analyses of mtDNA Supergenes……Page 430
7. EVOLUTION OF THE HUMAN MITOCHONDRIAL GENOME……Page 433
㠀⸀ 䴀䤀吀伀䌀䠀伀一䐀刀䤀䄀䰀 䐀一䄀 䄀一䐀 䠀唀䴀䄀一 䐀䤀匀䔀䄀匀䔀匀……Page 437
㤀⸀ 䴀䤀吀伀䌀䠀伀一䐀刀䤀䄀䰀 匀倀䔀䌀䤀䄀䰀䤀娀䔀䐀 䐀䄀吀䄀䈀䄀匀䔀匀……Page 442
䄀䌀䬀一伀圀䰀䔀䐀䜀䔀䴀䔀一吀匀……Page 446
刀䔀䘀䔀刀䔀一䌀䔀匀……Page 447
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Z……Page 510
Appendix 2: A Dictionary of Programs for Sequence Analysis……Page 512
APPENDIX REFERENCES……Page 540
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E……Page 551
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H……Page 554
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M……Page 556
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P……Page 560
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S……Page 564
T……Page 567
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Z……Page 569
Back Page……Page 570
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