Bioinformatics: A Practical Guide to the Analysis of Genes and Proteins, 2nd Edition

by Andreas D. Baxevanis (Genome Technology Branch, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland); B. F. Francis Ouellette (Centre for Molecular Medicine and Therapeutics, Children's and Women's Health Centr

• ISBN13: 9780471383918
• ISBN10: 0471383910
• Format: Paperback
• Copyright: 2001-01-01
• Publisher: Wiley-Interscience

Summary

Bioinformatics, Third Edition is essential reading for researchers, instructors, and students of all levels in molecular biology and bioinformatics, as well as for investigators involved in genomics, clinical research, proteomics, and computational biology.

Table of Contents

Foreword	xiii
Preface	xv
Contributors	xvii
Bioinformatics and the Internet	1	(18)
Andreas D. Baxevanis
Internet Basics	2	(2)
Connecting to the Internet	4	(3)
Electronic Mail	7	(3)
File Transfer Protocol	10	(3)
The World Wide Web	13	(3)
Internet Resources for Topics Presented in Chapter 1	16	(1)
References	17	(2)
The NCBI Data Model	19	(26)
James M. Ostell
Sarah J. Wheelan
Jonathan A. Kans
Introduction	19	(5)
PUBs: Publications or Perish	24	(4)
SEQ-Ids: What's in a Name?	28	(3)
BIOSEQs: Sequences	31	(3)
BIOSEQ-SETs: Collections of Sequences	34	(1)
SEQ-ANNOT: Annotating the Sequence	35	(5)
SEQ-DESCR: Describing the Sequence	40	(1)
Using the Model	41	(2)
Conclusions	43	(1)
References	43	(2)
The Genbank Sequence Database	45	(20)
Ilene Karsch-Mizrachi
B. F. Francis Ouellette
Introduction	45	(2)
Primary and Secondary Databases	47	(1)
Format vs. Content: Computers vs. Humans	47	(2)
The Database	49	(1)
The GenBank Flatfile: A Dissection	49	(9)
Concluding Remarks	58	(1)
Internet Resources for Topics Presented in Chapter 3	58	(1)
References	59	(1)
Appendices	59	(6)
Appendix 3.1 Example of GenBank Flatfile Format	59	(2)
Appendix 3.2 Example of EMBL Flatfile Format	61	(2)
Appendix 3.3 Example of a Record in CON Division	63	(2)
Submitting DNA Sequences to the Databases	65	(18)
Jonathan A. Kans
B. F. Francis Ouellette
Introduction	65	(1)
Why, Where, and What to Submit?	66	(1)
DNA/RNA	67	(2)
Population, Phylogenetic, and Mutation Studies	69	(1)
Protein-Only Submissions	69	(1)
How to Submit on the World Wide Web	70	(1)
How to Submit with Sequin	70	(7)
Updates	77	(1)
Consequences of the Data Model	77	(2)
EST/STS/GSS/HTG/SNP and Genome Centers	79	(1)
Concluding Remarks	79	(1)
Contact Points for Submission of Sequence Data to DDBJ/EMBL/GenBank	80	(1)
Internet Resources for Topics Presented in Chapter 4	80	(1)
References	81	(2)
Structure Databases	83	(28)
Christopher W. V. Hogue
Introduction to Structures	83	(4)
PDB: Protein Data Bank at the Research Collaboratory for Structural Bioinformatics (RCSB)	87	(4)
MMDB: Molecular Modeling Database at NCBI	91	(3)
Stucture File Formats	94	(1)
Visualizing Structural Information	95	(5)
Database Structure Viewers	100	(3)
Advanced Structure Modeling	103	(1)
Structure Similarity Searching	103	(3)
Internet Resources for Topics Presented in Chapter 5	106	(1)
Problem Set	107	(1)
References	107	(4)
Genomic Mapping And Mapping Databases	111	(44)
Peter S. White
Tara C. Matise
Interplay of Mapping and Sequencing	112	(1)
Genomic Map Elements	113	(2)
Types of Maps	115	(5)
Complexities and Pitfalls of Mapping	120	(2)
Data Repositories	122	(5)
Mapping Projects and Associated Resources	127	(15)
Practical Uses of Mapping Resources	142	(4)
Internet Resources for Topics Presented in Chapter 6	146	(2)
Problem Set	148	(1)
References	149	(6)
Information Retrieval From Biological Databases	155	(32)
Andreas D. Baxevanis
Integrated Information Retrieval: The Entrez System	156	(16)
LocusLink	172	(6)
Sequence Databases Beyond NCBI	178	(3)
Medical Databases	181	(2)
Internet Resources for Topics Presented in Chapter 7	183	(1)
Problem Set	184	(1)
References	185	(2)
Sequence Alignment and Database Searching	187	(28)
Gregory D. Schuler
Introduction	187	(1)
The Evolutionary Basis of Sequence Alignment	188	(2)
The Modular Nature of Proteins	190	(3)
Optimal Alignment Methods	193	(2)
Substitution Scores and Gap Penalties	195	(3)
Statistical Significance of Alignments	198	(1)
Database Similarity Searching	198	(2)
FASTA	200	(2)
BLAST	202	(2)
Database Searching Artifacts	204	(4)
Position-Specific Scoring Matrices	208	(1)
Spliced Alignments	209	(1)
Conclusions	210	(2)
Internet Resources for Topics Presented in Chapter 8	212	(1)
References	212	(3)
Creation and Analysis of Protein Multiple Sequence Alignments	215	(18)
Geoffrey J. Barton
Introduction	215	(1)
What is a Multiple Alignment, and Why Do It?	216	(1)
Structural Alignment or Evolutionary Alignment?	216	(1)
How to Multiply Align Sequences	217	(5)
Tools to Assist the Analysis of Multiple Alignments	222	(5)
Collections of Multiple Alignments	227	(1)
Internet Resources for Topics Presented in Chapter 9	228	(1)
Problem Set	229	(1)
References	230	(3)
Predictive Methods Using DNA Sequences	233	(20)
Andreas D. Baxevanis
GRAIL	235	(1)
Fgeneh/Fgenes	236	(2)
MZEF	238	(2)
GENSCAN	240	(1)
POCRUSTES	241	(5)
How Well Do the Methods Work?	246	(2)
Strategies and Considerations	248	(2)
Internet Resources for Topics Presented in Chapter 10	250	(1)
Problem Set	251	(1)
References	251	(2)
Predictive Methods Using Protein Sequences	253	(30)
Sharmila Banerjee-Basu
Andreas D. Baxevanis
Protein Identity Based on Composition	254	(3)
Physical Properties Based on Sequence	257	(2)
Motifs and Patterns	259	(4)
Secondary Structure and Folding Classes	263	(6)
Specialized Structures or Features	269	(5)
Tertiary Structure	274	(3)
Internet Resources for Topics Presented in Chapter 11	277	(1)
Problem Set	278	(1)
References	279	(4)
Expressed Sequence Tags (ESTs)	283	(20)
Tyra G. Wolfsberg
David Landsman
What is an EST?	284	(4)
EST Clustering	288	(5)
TIGR Gene Indices	293	(1)
STACK	293	(1)
ESTs and Gene Discovery	294	(1)
The Human Gene Map	294	(1)
Gene Prediction in Genomic DNA	295	(1)
ESTs and Sequence Polymorphisms	296	(1)
Assessing Levels of Gene Expression Using ESTs	296	(2)
Internet Resources for Topics Presented in Chapter 12	298	(1)
Problem Set	298	(1)
References	299	(4)
Sequence Assembly and Finishing Methods	303	(20)
Rodger Staden
David P. Judge
James K. Bonfield
The Use of Base Cell Accuracy Estimates or Confidence Values	305	(1)
The Requirements for Assembly Software	306	(1)
Global Assembly	306	(1)
File Formats	307	(1)
Preparing Readings for Assembly	308	(3)
Introduction to Gap4	311	(1)
The Contig Selector	311	(1)
The Contig Comparator	312	(1)
The Template Display	313	(3)
The Consistency Display	316	(1)
The Contig Editor	316	(3)
The Contig Joining Editor	319	(1)
Disassembling Readings	319	(1)
Experiment Suggestion and Automation	319	(2)
Concluding Remarks	321	(1)
Internet Resources for Topics Presented in Chapter 13	321	(1)
Problem Set	322	(1)
References	322	(1)
Phylogenetic Analysis	323	(36)
Fiona S. L. Brinkman
Detlef D. Leipe
Fundamental Elements of Phylogenetic Models	325	(2)
Tree Interpretation---The Importance of Identifying Paralogs and Orthologs	327	(1)
Phylogenetic Data Analysis: The Four Steps	327	(2)
Alignment: Building the Data Model	329	(4)
Alignment: Extraction of a Phylogenetic Data Set	333	(2)
Determining the Substitution Model	335	(5)
Tree-Building Methods	340	(5)
Distance, Parsimony, and Maximum Likelihood: What's the Difference?	345	(1)
Tree Evaluation	346	(2)
Phylogenetics Software	348	(6)
Internet-Accessible Phylogenetic Analysis Software	354	(2)
Some Simple Practical Considerations	356	(1)
Internet Resources for Topics Presented in Chapter 14	356	(1)
References	357	(2)
Comparative Genome Analysis	359	(34)
Michael Y. Galperin
Eugene V. Koonin
Progress in Genome Sequencing	360	(6)
Genome Analysis and Annotation	366	(16)
Application of Comparative Genomics---Reconstruction of Metabolic Pathways	382	(3)
Avoiding Common Problems in Genome Annotation	385	(2)
Conclusions	387	(1)
Internet Resources for Topics Presented in Chapter 15	387	(2)
Problems for Additional Study	389	(1)
References	390	(3)
Large-Scale Genome Analysis	393	(20)
Paul S. Meltzer
Introduction	393	(1)
Technologies for Large-Scale Gene Expression	394	(5)
Computational Tools for Expression Analysis	399	(8)
Hierarchical Clustering	407	(2)
Prospects for the Future	409	(1)
Internet Resources for Topics Presented in Chapter 16	410	(1)
References	410	(3)
Using Perl to Facilitate Biological Analysis	413	(38)
Lincoln D. Stein
Getting Started	414	(2)
How Scripts Work	416	(1)
Strings, Numbers, and Variables	417	(1)
Arithmetic	418	(1)
Variable Interpolation	419	(1)
Basic Input and Output	420	(2)
Filehandles	422	(2)
Making Decisions	424	(3)
Conditional Blocks	427	(3)
What is Truth?	430	(1)
Loops	430	(2)
Combining Loops with Input	432	(1)
Standard Input and Output	433	(2)
Finding the Length of a Sequence File	435	(1)
Pattern Matching	436	(4)
Extracting Patterns	440	(1)
Arrays	441	(3)
Arrays and Lists	444	(1)
Split and Join	444	(1)
Hashes	445	(1)
A Real-World Example	446	(3)
Where to Go From Here	449	(1)
Internet Resources for Topics Presented in Chapter 17	449	(1)
Suggested Reading	449	(2)
Glossary	451	(6)
Index	457