Bioinformatics: Sequence, Structure and Databanks A Practical Approach

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ISBN: 9780199637904 | 0199637903
Cover: Paperback
Copyright: 11/16/2000

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This volume covers practical important topics in the analysis of protein sequences and structures. It includes comparing amino acid sequences to structures comparing structures to each other, searching information on entire protein families as well as searching with single sequences, how to use the Internet and how to set up and use the SRS molecular biology database management system. Finally, there are chapters on multiple sequence alignment and protein secondary structure prediction. This book will be invaluable to occasional users of these techniques as well as experienced professionals or researchers.

Preface

List of protocols

xvii

Abbreviations

xix

Threading methods for protein structure prediction

(14)

David Jones

Caroline Hadley

Introduction

(1)

Threading methods

(7)

1-D-3-D profiles: Bowie et al. (1991)

(1)

Threading: Jones et al. (1992)

(2)

Protein fold recognition using secondary structure predictions: Rost (1997)

(1)

Combining sequence similarity and threading: Jones (1999)

(1)

Assessing the reliability of threading methods

(3)

Alignment accuracy

(1)

Post-processing threading results

(1)

Why does threading work?

(1)

Limitations: strong and weak fold-recognition

(1)

The domain problem in threading

(1)

The future

(3)

References

(3)

Comparison of protein three-dimensional structures

(36)

Mark S. Johnson

Jukka V. Lehtonen

Introduction

(1)

The comparison of protein structures

(15)

General considerations

(1)

What atoms/features of protein structure to compare?

(3)

Standard methods for finding the translation vector and rotation matrix

(5)

Standard methods to determine equivalent matched atoms between structures

(4)

Quality and extent of structural matches

(2)

The comparison of identical proteins

(1)

Why compare identical proteins?

(1)

Comparisons

(1)

The comparison of homologous structures: example methods

(10)

Background

(2)

Methods that require the assignment of seed residues

(1)

Automatic comparison of 3-D structures

(6)

Multiple structural comparisons

(1)

The comparison of unrelated structures

(4)

Background

(4)

Large-scale comparisons of protein structures

(5)

References

(3)

Multiple alignments for structural, functional, or phylogenetic analyses of homologous sequences

(26)

L. Duret

S. Abdeddaim

Introduction

(2)

Basic concepts for multiple sequence alignment

(3)

Homology: definition and demonstration

(1)

Global or local alignments

(1)

Substitution matrices, weighting of gaps

(2)

Searching for homologous sequences

(1)

Multiple alignment methods

(12)

Optimal methods for global multiple alignments

(2)

Progressive global alignment

(2)

Block-based global alignment

(2)

Motif-based local multiple alignments

(1)

Comparison of different methods

(3)

Particular case: aligning protein-coding DNA sequences

(1)

Visualizing and editing multiple alignments

(3)

Manual expertise to check or refine alignments

(1)

Annotating alignments, extracting sub-alignments

(1)

Comparison of alignment editors

(1)

Alignment shading software, pretty printing, logos, etc.

(1)

Databases of multiple alignments

(1)

Summary

(4)

References

(3)

Hidden Markov models for database similarity searches

(16)

Ewan Birney

Introduction

(1)

Overview

(1)

Using profile and profile-HMM databases

(2)

Pfam

(1)

Prosite profiles

(1)

SMART

(1)

Other resources and future directions

(1)

Limitations of profile-HMM databases

(1)

Using PSI-BLAST

(1)

Using HMMER2

(3)

Overview of using HMMER

(1)

Making the first alignment

(1)

Making a profile-HMM from an alignment

(1)

Finding homologues and extending the alignment

(1)

False positives

(1)

Validating a profile-HMM match

(1)

Practical issues of the theories behind profile-HMMs

(7)

Overview of profile-HMMs

(1)

Statistics for profile-HMM

(2)

Profile-HMM construction

(1)

Priors and evolutionary information

(1)

Technical issues

(1)

References

(2)

Protein family-based methods for homology detection and analysis

(20)

Steven Henikoff

Jorja Henikoff

Introduction

(2)

Expanding protein families

(1)

Terms used to describe relationships among proteins

(1)

Alternative approaches to inferring function from sequence alignment

(1)

Displaying protein relationships

(3)

From pairwise to multiple-sequence alignments

(1)

Patterns

(1)

Logos

(1)

Trees

(1)

Block-based methods for multiple-sequence alignment

(3)

Pairwise alignment-initiated methods

(1)

Pattern-initiated methods

(1)

Iterative methods

(1)

Implementations

100

(1)

Position-specific scoring matrices (PSSMs)

101

(2)

Sequence weights

102

(1)

PSSM column scores

102

(1)

Searching family databases with sequence queries

103

(5)

Curated family databases: Prosite, Prints, and Pfam

105

(1)

Clustering databases: ProDom, DOMO, Protomap, and Prof pat

105

(1)

Derived family databases: Blocks and Proclass

106

(1)

Other tools for searching family databases

107

(1)

Searching with family-based queries

108

(5)

Searching with embedded queries

108

(1)

Searching with PSSMs

108

(1)

Iterated PSSM searching

109

(1)

Multiple alignment-based searching of protein family databases

110

(1)

References

110

(3)

Predicting secondary structure from protein sequences

113

(30)

Jaap Heringa

Introduction

113

(5)

What is secondary structure?

113

(1)

Where could knowledge about secondary structure help?

114

(1)

What signals are there to be recognized?

114

(4)

Assessing prediction accuracy

118

(2)

Prediction methods for globular proteins

120

(13)

The early methods

120

(2)

Accuracy of early methods

122

(1)

Other computational approaches

122

(1)

Prediction from multiply-aligned sequences

123

(6)

A consensus approach: JPRED

129

(2)

Multiple-alignment quality and secondary-structure prediction

131

(1)

Iterated multiple-alignment and secondary structure prediction

132

(1)

Prediction of transmembrane segments

133

(4)

Prediction of α-helical TM segments

134

(2)

Orientation of transmembrane helices

136

(1)

Prediction of α-strand transmembrane regions

136

(1)

Coiled-coil structures

137

(1)

Threading

138

(1)

Recommendations and conclusions

138

(5)

References

139

(4)

Methods for discovering conserved patterns in protein sequences and structures

143

(24)

Inge Jonassen

Introduction

143

(1)

Pattern descriptions

144

(10)

Exact or approximate matching

144

(1)

PROSITE patterns

145

(1)

Alignments, profiles, and hidden Markov models

146

(2)

Pattern significance

148

(2)

Pattern databases

150

(3)

Using existing pattern collections

153

(1)

Finding new patterns

154

(2)

A general approach

154

(1)

Discovery algorithms

155

(1)

The Pratt programs

156

(6)

Using Pratt

157

(2)

Pratt: Internal search methods

159

(2)

Scoring patterns

161

(1)

Structure motifs

162

(2)

The SPratt program

162

(2)

Examples

164

(1)

Conclusions

164

(3)

References

165

(2)

Comparison of protein sequences and practical database searching

167

(24)

Golan Yona

Steven E. Brenner

Introduction

167

(1)

Alignment of sequences

168

(5)

Rigorous alignment algorithms

169

(2)

Heuristic algorithms for sequence comparison

171

(2)

Probability and statistics of sequence alignments

173

(5)

Statistics of global alignment

174

(1)

Statistics of local alignment without gaps

175

(2)

Statistics of local alignment with gaps

177

(1)

Practical database searching

178

(9)

Types of comparison

178

(1)

Databases

179

(2)

Algorithms

181

(1)

Filtering

181

(1)

Scoring matrices and gap penalties

182

(3)

Command line parameters

185

(2)

Interpretation of results

187

(1)

Conclusion

188

(3)

References

188

(3)

Networking for the biologist

191

(24)

R. A. Harper

Introduction

191

(1)

The changing face of networking

192

(11)

Networking in Europe

194

(1)

The way we were...e-mail servers for sequence retrieval

195

(4)

Similarity searches via e-mail

199

(2)

Speed solutions for similarity searches

201

(2)

Sequence retrieval via the WWW

203

(5)

Entrez from the NCBI

205

(1)

SRS from the EBI

205

(3)

Submitting sequences

208

(4)

Bankit at NCBI

209

(1)

Sequin from NCBI

209

(1)

Webin from EBI

210

(2)

Sakura from DDJB

212

(1)

Conclusions

212

(3)

References

213

(2)

SRS---Access to molecular biological databanks and integrated data analysis tools

215

(28)

D. P. Kreil

T. Etzold

Introduction

215

(2)

SRS fills a critical need

215

(1)

History, philosophy, and future of SRS

216

(1)

A user's primer

217

(8)

A simple query

219

(1)

Exploiting links between databases

220

(1)

Using Views to explore query results

221

(2)

Launching analysis tools

223

(2)

Overview

225

(1)

Advanced tools and concepts

225

(11)

Refining queries

225

(5)

Creating custom Views

230

(2)

SRS world wide: using DATABANKS

232

(1)

Interfacing with SRS over the network

233

(3)

SRS server side

236

(4)

User's point of view

236

(2)

Administrator's point of view

238

(2)

Where to turn to for help

240

(3)

Acknowledgements

241

(1)

References

241

(2)

List of suppliers

243

(4)

Index

247

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Bioinformatics: Sequence, Structure and Databanks A Practical Approach

Summary

Table of Contents

Supplemental Materials