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DNA and Protein Sequence Analysis: A Practical Approach [Hardback]

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  • Formāts: Hardback, 373 pages, height x width: 230x150 mm, weight: 760 g, 2 colour illustrations, 1 halftone, 69 line figures, bibliography
  • Sērija : A Practical Approach No.171
  • Izdošanas datums: 01-Jan-1997
  • Izdevniecība: Oxford University Press
  • ISBN-10: 0199634645
  • ISBN-13: 9780199634644
Citas grāmatas par šo tēmu:
DNA and Protein Sequence Analysis: A Practical Approach
  • Formāts: Hardback, 373 pages, height x width: 230x150 mm, weight: 760 g, 2 colour illustrations, 1 halftone, 69 line figures, bibliography
  • Sērija : A Practical Approach No.171
  • Izdošanas datums: 01-Jan-1997
  • Izdevniecība: Oxford University Press
  • ISBN-10: 0199634645
  • ISBN-13: 9780199634644
Citas grāmatas par šo tēmu:
Permanent link: https://www.kriso.lv/db/9780199634644.html
Keywords:
This text focuses on sequence data - either lists of nucleotides or of amino acids - which are nowadays easily gathered using automated equipment. The real effort is involved in interpreting the data to produce predictions of protein structure or function. With the advent of worldwide computer networks, a plethora of software is now available for sequence analysis. This describes the techniques for computer analysis of sequence data, with the emphasis on general issues rather than specific algorithms. It is a revision of the 1987 IRL Press book, Nucleic Acid and Protein Sequence Analysis , by the same editors. It is aimed at post-graduate, post-doctoral researchers, and academic staff in the general area of protein science.
List of contributors xxi(2) Abbreviations xxiii
1. Molecular biology databases 1(30) Christian Burks
1. Overview 1(15) Summary 1(1) Molecular biology databases 2(1) Sequence databases 2(14) What are the uses of databases? 16(1)
2. Contributing data to the databases 16(3) Community pipelines 16(1) Direct, electronic submission 17(1) Timeliness of release of data to databanks 17(1) Promulgating data revisions and extensions 18(1)
3. Retrieving data from the databases 19(5) Finding databases of interest 19(3) Media 22(1) Mechanisms 22(1) Which databases should I get? 23(1)
4. Using the data 24(2) Do I have a current version of the database? 24(1) How often should I repeat routine queries 24(1) How redundant is the database? 25(1) Are there errors in the database? 25(1) How did I get that result? 26(1)
5. Queries across multiple databases 26(2)
6. Keeping up and going further 28(1) Acknowledgements 29(1) References 29(2)
2. The NCBI software tools 31(14) J. M. Ostell
1. Introduction 31(1)
2. The software toolkit 31(1) Portable core library 31(1) Data encoding in ASN.1 32(1)
3. The NCBI data model 32(7) Introduction 32(1) Pub 33(1) Bioseq 34(5)
4. Technical aspects of the NCBI toolkit 39(3) ASN.1 libraries 39(1) Object loader layer 39(1) Utilities layer 39(1) Access libraries 40(1) Vibrant portable graphical interface 40(1) Network client/server libraries 41(1)
5. NCBI toolkit applications 42(1) Entrez 42(1) BLAST 42(1) BankIt 42(1) Sequin 42(1) Others 42(1)
6. Summary 42(3)
3. EBI databases and tools 45(14) Rainer Fuchs Graham N. Cameron
1. EBI information products 45(1)
2. Databases and software on the EBI CD-ROM 46(5) EBI software for DOS computers 48(1) EBI retrieval software for Macintosh computers 49(2) Other software 51(1)
3. Network information services 51(5) EBI database and information servers 51(3) On-line database access 54(2) Remote database searches 56(1)
4. Contacting the EBI 56(2) Acknowledgements 58(1) References 58(1)
4. Networked services 59(16) G. Williams
1. Introduction 59(1) Logging in to the system 59(1) Computer names 59(1)
2. Electronic mail 60(1) E-mail 60(1) E-mail servers 60(1)
3. File transfer protocol (FTP) 61(3) FTP 61(2) File formats 63(1) Archie 64(1)
4. Remote log in 64(2) Telnet 64(1) BIDS 65(1) MEDLARS 65(1) MSDN 66(1)
5. Mailing lists and network news 66(4) Mailing lists 67(1) Usenet/network news 68(2)
6. Information servers 70(4) Gopher 70(1) WWW 70(4)
7. Further information 74(1) References 74(1)
5. DNA sequencing methodology and software 75(24) William D. Rawlinson Barclay G. Barrell
1. Introduction 75(1)
2. DNA sequencing methods 76(2)
3. Sequence handling software and sequence project design 78(4) Conventions 79(1) Display of trace data from within the database 80(1) Software created to make design of sequencing reactions easier 80(2)
4. The software for assembling sequence data 82(12) The database assembly and handling program (xbap) 82(11) Alternative packages 93(1)
5. Assessment of sequencing projects 94(1) Recording information about the sequencing templates 94(1) Assessment of the sequence data during assembly 94(1)
6. Discussion 95(2) Acknowledgements 97(1) References 97(2)
6. Molecular biology software for the Apple Macintosh 99(38) M. Ginsburg M. P. Mitchell
1. Introduction 99(1)
2. GeneWorks 100(11) Overview 100(1) DNA analysis 101(3) Protein analysis 104(4) Special analyses 108(3)
3. MacVector suite 111(8) Overview 111(1) DNA analysis 112(3) Protein analysis 115(2) Special analyses 117(2) AssemblyLIGN 119(1)
4. DNAStar 119(7) Overview 119(1) Sequence editing 120(1) Pattern analysis 121(1) Protein analysis 122(1) Special analyses 123(3)
5. Sequencher 126(2) Overview 126(1) Entering sequences 127(1) Assembling the data 127(1) Editing the data 128(1)
6. Amplify 128(2) Overview 128(1) Running the program 129(1)
7. MacPattern 130(2) Overview 130(1) Running the program 130(2)
8. Other programs 132(2) Suppliers 133(1) Internet Sources 134(1) References 134(3) Further reading 135(2)
7. Sequence comparison and alignment 137(32) Stephen F. Altschul
1. Introduction 137(1)
2. Global sequence alignment 137(4) Algorithms 137(2) Substitution and gap scores 139(1) Statistics 140(1)
3. Global multiple alignment 141(2) Scores 141(1) Algorithms 142(1)
4. Local sequence alignment 143(8) Algorithms 143(1) Local alignment statistics 144(4) Local alignment scoring systems 148(3)
5. Database search methods 151(3) Parallel architectures 151(1) Heuristic algorithms 152(2) Vector-based comparison methods 154(1)
6. Local multiple alignment 154(4) Consensus word methods 155(1) Template methods 156(1) Progressive alignment methods 156(1) Pairwise comparison methods 157(1) Statistically-based methods 157(1) General issues 158(1)
7. Sequence motifs 158(4) Weight matrices 159(3) Generalizations 162(1) Acknowledgements 162(1) References 162(7)
8. Simple sequences of protein and DNA 169(16) John C. Wootton
1. Introduction 169(1)
2. Some practical guidelines to a complex body of theory 170(5) Complexity, pattern, and periodicity are distinct properties of simple sequences 170(1) Terminology 171(1) Local compositional complexity 171(2) Low complexity is more clear-cut for proteins than DNA 173(1) Unbiased inference 173(1) Sources for mathematical background 173(1) Visual inspection is complementary to mathematical analysis 174(1)
3. Software and examples of applications 175(5) Available software 175(1) Comparison of different algorithms and programs 175(5) Future software developments 180(1)
4. Masking of low-complexity sequences for searching databases 180(1) The problem 180(1) Masking methods 180(1)
5. Complexity definitions and segmentation algorithm 181(1) Definition 1 181(1) Definition 2 181(1) Probabilities of complexity states 182(1) Segmentation algorithm based on compositional complexity 182(1) References 182(3)
9. Repetitive sequences in DNA 185(12) Jorg T. Epplen Olaf Riess
1. Introduction 185(2)
2. Types of repetitive sequences 187(2) Satellite DNA 187(1) Simple repetitive DNA sequences 188(1) Short and long interspersed nucleotide elements (SINEs and LINEs) 188(1) Minisatellites 189(1)
3. Repeats in genomic DNA (and protein) databanks 189(2) Evolutionary aspects 190(1) Expression of repeats 190(1) Repeats as tools 191(1)
4. Short consensus motifs for the identification of functional sequences in DNA which appear repetitively in and around genes 191(1)
5. Diseases caused by expansion of simple nucleotide repeats 192(1)
6. Conclusions 193(1) References 193(4)
10. Isochores and synonymous substitutions in mammalian genes 197(12) Giorgio Bernardi Dominique Mouchiroud Christian Gautier
1. Introduction 197(1)
2. Methods 198(1)
3. Results 198(5)
4. Discussion 203(4) The frequencies of synonymous substitutions do not exhibit differences related to regions of the mammalian genome 203(1) Differences in repair efficiency do not cause differences in the rates of synonymous substitutions of genes located in different isochore families 204(1) Differences in the process of mutation associated with replication timing do not affect the rates nor the biases of synonymous substitutions of genes located in different isochore families 205(1)
5. Conclusions 206(1) References 207(2)
11. Identifying genes in genomic DNA sequences 209(16) Eric E. Snyder Gary D. Stormo
1. Introduction 209(3) Low-level motif identification 210(1) Assembling complete genes using multiple pieces of evidence 211(1)
2. Programs 212(3) GeneModeler 212(1) GeneID 213(1) GRAIL 214(1) GeneParser 215(1)
3. Performance statistics 215(5) Test data 216(2) Comparison of currently available programs 218(1) Results 219(1)
4. Recommendations for users 220(3)
5. Conclusions 223(1) References 223(2)
12. Prediction of mRNA sequence function 225(6) Keith Vass
1. Introduction 225(1)
2. Analysis of sequence data 226(4) Short sequence patterns 226(1) Repeated sequences 226(1) Conserved sequences 227(1) Database searching 228(1) Secondary structure 229(1) Secondary structure searches of sequence databases 230(1)
3. Summary 230(1) References 230(1)
13. Forecasting protein function 231(24) T. C. Hodgman
1. Introduction 231(1)
2. Structure/function relationships 232(1)
3. General strategy 233(1)
4. Pairwise domain matches 234(5) FASTA and BLAST 235(2) MPSRCH and PROSRCH 237(1) DFLASH 238(1) Assessing retained sequences 238(1)
5. Weak domain matches 239(3) General points 239(1) SBASE 240(1) PRODOM 240(1) PLSEARCH 240(2) BLAST3 242(1)
6. Motif matches 242(4) Sources 242(1) Definitions 242(2) PROSEARCH 244(1) BLOCKS 244(1) BLA 245(1) LUPES 246(1)
7. URF alignments 246(2) PROFILESEARCH 247(1) PIPL 247(1) PTNSRCH 247(1) SCRUTINEER 247(1)
8. Assessing candidate matches 248(1)
9. Single sequence analyses 249(2) Repeats 249(1) Biased composition 249(1) Secondary structure 250(1)
10. Software sources 251(1) Acknowledgements 252(1) References 253(2)
14. DNA and RNA structure prediction 255(24) Eric Westhof Pascal Auffinger Christine Gaspin
1. Introduction 255(2)
2. Molecular mechanics and molecular dynamics methods 257(4) The potential energy function 257(2) Molecular dynamics simulation protocols 259(2) Modelling large nucleic acids 261(1) Analysis of the trajectories 261(1)
3. Fine structure and the search for specific regions in DNA 261(1)
4. RNA secondary structure prediction 262(10) Representation 263(1) Data necessary for folding RNA molecules 264(2) Methods of prediction 266(6) Limits 272(1)
5. RNA tertiary structure construction 272(1)
6. Conclusions 273(1) Acknowledgements 273(2) References 275(4)
15. Phylogenetic estimation 279(34) Nick Goldman
1. Introduction 279(2)
2. Common ground 281(6) Trees 281(1) Data 282(1) Models of evolutionary change 283(3) Estimation 286(1) Heuristics 287(1)
3. Phylogenetic estimation methods based on sequences 287(6) Maximum likelihood methods 287(4) Parsimony methods 291(2)
4. Phylogenetic estimation methods based on distances 293(4) Sequence distances 294(1) Phylogenetic trees from distance matrices 295(2)
5. Comparison of methods 297(2)
6. Other phylogenetic estimation methods 299(2) Lakes method of invariants 300(1) Heins method of simultaneous alignment and phylogenetic tree estimation 300(1) Minimum message length coding 301(1)
7. Measuring uncertainty 301(5) Statistical fluctuation 302(3) Systematic errors 305(1)
8. The future of phylogenetic estimation 306(2)
9. Appendix: computer programs 308(3) PHYLIP 308(1) MEGA 309(1) PAUP 309(1) BASEML and BASEMLG 310(1) PROTML 310(1) TREEALIGN 310(1) Minimum message length encoding 310(1) FASTDNAML 310(1) References 311(2)
16. Evolution and relationships of protein families 313(28) William R. Taylor
1. Introduction 313(1)
2. Sequence similarity 314(8) Pairwise sequence alignment 314(4) Multiple sequence alignments 318(1) Structure biased alignment 319(2) Sequence threading 321(1)
3. Structural comparison 322(6) Recent comparison methods 323(1) Fold classification 324(2) How many protein folds? 326(2)
4. Molecular evolution 328(7) Genetic algorithm model 328(1) Gene duplication and fusion 329(1) Introns and exons 330(2) Evolution of function 332(3)
5. Theory 335(1)
6. Conclusions 336(1) References 336(5) A1. List of suppliers 341(2) Glossary 343(6) Index 349