Data Analysis in Molecular Biology and Evolution

by Xia, Xuhua

• ISBN13: 9780792375005
• ISBN10: 0792375009
• Format: Paperback
• Copyright: 2001-09-01
• Publisher: Kluwer Academic Pub

Summary

Data Analysis in Molecular Biology and Evolution introduces biologists to DAMBE, a proprietary, user-friendly computer program for molecular data analysis. The unique combination of this book and software will allow biologists not only to understand the rationale behind a variety of computational tools in molecular biology and evolution, but also to gain instant access to these tools for use in their laboratories. Data Analysis in Molecular Biology and Evolution serves as an excellent resource for advanced level undergraduates or graduates as well as for professionals working in the field.

Author Biography

Dr. Xuhua Xia is affiliated with the University of Hong Kong and specializes in bioinformatics.

Table of Contents

ACKNOWLEDGEMENTS	xi
PREFACE	xiii
1. INSTALLATION OF DAMRE AND A QUICK START	1	(1)
1. INSTALLATION	1	(1)
2. A JUMP START	2
2. FILE CONVERSION	1	(16)
1. A PLETHORA OF COMPUTER PROGRAMS	8	(1)
2. A PLETHORA OF SEQUENCE FORMATS	8	(1)
3. READSEQ	9	(1)
4. FILE CONVERSION USING DAMBE	10	(7)
4.1 Convert all sequences from one format to another	11	(1)
4.2 Converting a subset of sequences	12	(1)
4.3 Output PHYLTEST frles	13	(4)
3. PROCESSING GENBANK FILES	17	(8)
1. GENBANK FILE FORMAT	18	(2)
2. REANDING GENBANK FILES WITH DAMRE	20	(5)
4. ACCESSING GENBANK OR NETWORKED COMPUTERS	25	(8)
1. INTRODUCTION	25	(1)
2. READING MOLECULAR SEQUENCES DIRECTLY FROM GENBANK	25	(5)
3. READING FROM AND WRITING TO ANOTHER NETWORKED COMPUTER	30	(2)
4. EXERCISE	32	(1)
5. PAIR-WISE AND MULTIPLE SEQUENCE ALIGNMENT	33	(8)
1. INTRODUCTION	33	(4)
1.1 The dot-matrix approach	33	(3)
1.2 Similarity or distance method	36	(1)
2. SEQUENCE ALIGNMENT USING DAMBE	37	(4)
2.1 Align nucleotide or amino acid sequences	37	(1)
2.2 Align nucleotide sequences against amino acid sequences	38	(3)
6. FACTORS AFFECTING NUCLEOTIDE FREQUENCIES	41	(8)
1. INTRODUCTION	41	(3)
1.1 The frequency parameters	41	(1)
1.2 Factors that might change the frequency parameters	42	(1)
1.3 Frequency parameters and phylogenetic analyses	43	(1)
2. COUNTING NUCLEOTIDE AND DINUCLEOTIDE FREQUENCIES	44	(5)
7. CASE STUDY 1: ARTHROPOD PHYLOGENY	49	(10)
1. INTRODUCTION	49	(1)
2. OBTAIN DATA FROM GENBANK	50	(3)
3. ALIGN THE SEQUENCES	53	(3)
4. DATA ANALYSIS	56	(3)
8. FACTORS AFFECTING CODON FREQUENCIES	59	(12)
1. INTRODUCTION	59	(1)
2. GENERATING CODON USAGE TABLE WITH DAMBE	60	(4)
3. DNA METHYLATION AND USAGE OF ARGININE CODONS	64	(2)
4. TRANSCRIPTION EFFICIENCY AND CODON USAGE BIAS	66	(1)
5. TRANSLATIONAL EFFICIENCY AND CODON USAGE BIAS	66	(2)
6. CODON FREQUENCY AND PEPTIDE LENGTH IN ANCIENT PROTEINS	68	(3)
9. CASE STUDY 2: TRANSCRIPTION AND CODON USAGE BIAS	71	(20)
1. INTRODUCTION	71	(1)
2. MAXIMIZING TRANSCRIPTIONAL EFFICIENCY	72	(3)
3. PREDICTIONS AND EMPIRICAL TESTS	75	(10)
4. AN ALTERNATIVE EXPLANATION	85	(4)
5. DISCUSSION	89	(2)
10. CASE STUDY 3: TRANSLATION AND CODON USAGE BIAS	91	(16)
1. INTRODUCTION	91	(1)
2. THE ELONGATION MODEL, ITS PREDICTIONS, AND EMPIRICAL TESTS	92	(11)
2.1 Adaptation of Codon Usage to tRNA Content	94	(4)
2.2 Adaptation of tRNA to Codon Usage	98	(1)
2.3 Evolution of tRNA in Response to Amino Acid Usage	99	(3)
2.4 Translational Efficiency and Translational Accuracy	102	(1)
3. Discussion	103	(4)
3.1 Validity of the Model	103	(1)
3.2 Translational Efficiency and Accuracy on Codon Usage Bias	104	(1)
3.3 How Optimised Are the Translational Machinery?	105	(2)
11. EVOLUTION OF AMINO ACID USAGE	107	(8)
1. INTRODUCTION	107	(2)
2. AMINO ACID USAGE BIAS	109	(6)
12. PATTERN OF NUCLEOTIDE SUBSTITUTIONS	115	(10)
1. INTRODUCTION	115	(3)
2. USE DAMBE TO DOCUMENT EMPIRICAL SUBSTITUTION PATTERNS	118	(7)
2.1 Simple output
2.2 Detailed Output	119	(6)
13. PREAMBLE TO THE PATTERN OF CODON SUBSTITUTION	125	(6)
1. INTRODUCTION	125	(1)
2. DEFAULT SUBSTITUTION PATTERNS WITH NO SELECTION	126	(5)
14. FACTORS AFFECTING CODON SUBSTITUTIONS	131	(16)
1. INTRODUCTION	131	(5)
1.1 The Rate of Codon Substitutions and its Determinants	131	(1)
1.2 Models of Codon Substitution	132	(2)
1.3 The Expected Pattern of Nonsynonymous Codon Substitutions	134	(2)
2. CODON COMPARISON WITH DAMRE	136	(11)
2.1 Tracing evolutionary history	136	(4)
2.2 Summary of codon substitution pattern	140	(2)
2.3 Single-step Nonsynonymous Codon Substitutions	142	(5)
15. CASE STUDY 4: TRANSITION BIAS	147	(18)
1. INTRODUCTION	147	(4)
2. GET SEQUENCE DATA	151	(1)
3. DATA ANALYSIS	152	(8)
3.1 Phylogeny reconstruction	152	(5)
3.2 Pair-wise comparisons between neighboring nodes	157	(3)
4. RESULTS	160	(2)
5. DISCUSSION	162	(3)
16. SUBSTITUTION PATTERN IN AMINO ACID SEQUENCES	165	(6)
1. SUBSTITUTION PATTERN FROM SEQUENCES IN RST FORMAT	165	(4)
2. SUBSTITUTION PATTERN FROM ALL PAIR-WISE COMPARISONS	169	(2)
17. A STATISTICAL DIGRESSION	171	(8)
1. INTRODUCTION	171	(1)
2. TWO DISCRETE PROBABILITY DISTRIBUTIONS	172	(3)
2.1 The Binomial Distribution and the Goodness-of-fit test	172	(2)
2.2 The Multinormal Distribution	174	(1)
3. THE SIMPLEST PRESENTATION OF THE MAXIMUM LIKELIHOOD METHOD	175	(2)
4. BIAS IN THE MAXIMUM LIKELIHOOD METHOD	177	(1)
5. EXERCISE	178	(1)
18. THEORETICAL BACKGROUND OF GENETIC DISTANCES	179	(12)
1. INTRODUCTION	179	(1)
2. GENETIC DISTANCES FROM NUCLEOTIDE SEQUENCES	180	(7)
2.1 JC69 and TN84 distances	181	(2)
2.2 Kimura's two parameter distance	183	(1)
2.3 F84 distance	184	(1)
2.4 TN93 distance	185	(1)
2.5 Lake's paral meas distance	186	(1)
3. DISTANCES BASED ON CODON SEQUENCES	187	(5)
3.1 The empirical counting approach	188	(2)
3.2 Codon-based maximur likelihood method	190	(2)
4. DISTANCES BASED ON AMINO ACID SEQUENCES	192	(1)
5. GENETIC DISTANCES FROM ALLELE FREQUENCIES	193
5.1 Nei's genetic distance;	194	(1)
5.2 Cavalli-Sforza's chord measure	195	(1)
5.3 Reynolds, Weir, and Cockerham's genetic distance	196
19. MOLECULAR PHYLOGENETICS: CONCEPTS AND PRACTICE	191	(34)
1. THE MOLECULAR CLOCK AND ITS CALIBRATION	198	(6)
1.1 Calibrating a molecular clock	200	(1)
1.2 Complications in calibrating a molecular clock	201	(3)
2. COMMON APPROACHES IN MOLECULAR PHYLOGENETICS	204	(20)
2.1 Distance methods	204	(10)
2.2 Maximum parsimony method	214	(2)
2.3 Maximum likelihood method	216	(5)
2.4 Reconstructing Ancestral Sequences	221	(3)
3. EXERCISE	224	(1)
20. TESTING THE MOLECULAR CLOCK HYPOTHESIS	225	(8)
1. THE T-TEST	226
2. THE LIKELIHOOD RATIO TEST	221	(9)
3. TEST THE MOLECULAR CLOCK HYPOTHESIS	230	(3)
21. TESTING PHYLOGENETIC HYPOTHESES	233	(16)
1. BASIC STATISTICAL CONCEPTS	234	(2)
2. TESTING PHYLOGENETIC HYPOTHESES WITH THE DISTANCE METHOD	236	(5)
2.1 The Rationale	236	(2)
2.2 Test alternative phylogenetic hypotheses with the distance method	238	(3)
3. TESTING PHYLOGENETIC HYPOTHESES WITH THE PARSIMONY METHOD	241	(2)
4. TESTING PHYLOGENETIC HYPOTHESES WITH THE LIKELIHOOD METHOD	243	(4)
5. RESAMPLING METHODS	247	(1)
6. EXERCISE	248	(1)
22. FITTING PROBABILITY DISTRIBUTIONS	249	(16)
1. INTRODUCTION	249	(9)
1.1 The Poisson distribution	250	(2)
1.2 The negative binomial distribution	252	(2)
1.3 The gamma distribution	254	(3)
1.4 Some general guidelines forfitting statistical distributions	257	(1)
2. FITTING DISCRETE DISTRIBUTIONS WITH DAMRE,	258	(3)
3. ESTIMATING THE SHAPE PARAMETER OF THE GAMMA DISTRIBUTION	261	(2)
4. EXERCISE	263	(2)
LITERATURE CITED	265	(10)
INDEX	275