Bioinformatics: Sequence, Structure and Databanks A Practical Approach

by Higgins, Des; Taylor, Willie

• ISBN13: 9780199637904
• ISBN10: 0199637903
• Format: Paperback
• Copyright: 2000-11-16
• Publisher: Oxford University Press

Summary

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.

Table of Contents

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 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