Bioinformatics 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. Bioinformatics will be invaluable to occasional users of these techniques as well as experienced professionals or researchers.
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"a worthwhile addition to your library"R Briefings in Bioformatics
Preface v List of protocols xvii Abbreviations xix Threading methods for protein structure prediction 1(14) David Jones Caroline Hadley Introduction 1(1) Threading methods 1(7) 1-D-3-D profiles: Bowie et al. (1991) 5(1) Threading: Jones et al. (1992) 5(2) Protein fold recognition using secondary structure predictions: Rost (1997) 7(1) Combining sequence similarity and threading: Jones (1999) 7(1) Assessing the reliability of threading methods 8(3) Alignment accuracy 9(1) Post-processing threading results 10(1) Why does threading work? 10(1) Limitations: strong and weak fold-recognition 11(1) The domain problem in threading 11(1) The future 12(3) References 12(3) Comparison of protein three-dimensional structures 15(36) Mark S. Johnson Jukka V. Lehtonen Introduction 15(1) The comparison of protein structures 16(15) General considerations 16(1) What atoms/features of protein structure to compare? 17(3) Standard methods for finding the translation vector and rotation matrix 20(5) Standard methods to determine equivalent matched atoms between structures 25(4) Quality and extent of structural matches 29(2) The comparison of identical proteins 31(1) Why compare identical proteins? 31(1) Comparisons 31(1) The comparison of homologous structures: example methods 32(10) Background 32(2) Methods that require the assignment of seed residues 34(1) Automatic comparison of 3-D structures 35(6) Multiple structural comparisons 41(1) The comparison of unrelated structures 42(4) Background 42(4) Large-scale comparisons of protein structures 46(5) References 48(3) Multiple alignments for structural, functional, or phylogenetic analyses of homologous sequences 51(26) L. Duret S. Abdeddaim Introduction 51(2) Basic concepts for multiple sequence alignment 53(3) Homology: definition and demonstration 53(1) Global or local alignments 54(1) Substitution matrices, weighting of gaps 54(2) Searching for homologous sequences 56(1) Multiple alignment methods 57(12) Optimal methods for global multiple alignments 59(2) Progressive global alignment 61(2) Block-based global alignment 63(2) Motif-based local multiple alignments 65(1) Comparison of different methods 65(3) Particular case: aligning protein-coding DNA sequences 68(1) Visualizing and editing multiple alignments 69(3) Manual expertise to check or refine alignments 71(1) Annotating alignments, extracting sub-alignments 71(1) Comparison of alignment editors 72(1) Alignment shading software, pretty printing, logos, etc. 72(1) Databases of multiple alignments 72(1) Summary 73(4) References 74(3) Hidden Markov models for database similarity searches 77(16) Ewan Birney Introduction 77(1) Overview 78(1) Using profile and profile-HMM databases 79(2) Pfam 80(1) Prosite profiles 80(1) SMART 81(1) Other resources and future directions 81(1) Limitations of profile-HMM databases 81(1) Using PSI-BLAST 81(1) Using HMMER2 82(3) Overview of using HMMER 83(1) Making the first alignment 83(1) Making a profile-HMM from an alignment 84(1) Finding homologues and extending the alignment 84(1) False positives 85(1) Validating a profile-HMM match 85(1) Practical issues of the theories behind profile-HMMs 86(7) Overview of profile-HMMs 86(1) Statistics for profile-HMM 87(2) Profile-HMM construction 89(1) Priors and evolutionary information 89(1) Technical issues 90(1) References 91(2) Protein family-based methods for homology detection and analysis 93(20) Steven Henikoff Jorja Henikoff Introduction 93(2) Expanding protein families 93(1) Terms used to describe relationships among proteins 93(1) Alternative approaches to inferring function from sequence alignment 94(1) Displaying protein relationships 95(3) From pairwise to multiple-sequence alignments 95(1) Patterns 96(1) Logos 97(1) Trees 97(1) Block-based methods for multiple-sequence alignment 98(3) Pairwise alignment-initiated methods 98(1) Pattern-initiated methods 99(1) Iterative methods 99(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 users 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) Users point of view 236(2) Administrators 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
