Bioinformatics For Dummies

, by Claverie, Jean-Michel; Notredame, Cedric

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ISBN: 9780470089859 | 0470089857
Cover: Paperback
Copyright: 12/18/2006

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Were you always curious about biology but were afraid to sit through long hours of dense reading? Did you like the subject when you were in high school but had other plans after you graduated? Now you can explore the human genome and analyze DNA without ever leaving your desktop!Bioinformatics for Dummies is packed with valuable information that introduces you to this exciting new discipline. This easy-to-follow guide leads you step by step through every bioinformatics task that can be done over the Internet. Forget long equations, computer-geek gibberish, and installing bulky programs that slow down your computer. You'll be amazed at all the things you can accomplish just by logging on and following these trusty directions. You get the tools you need to: Analyze all types of sequences Use all types of databases Work with DNA and protein sequences Conduct similarity searches Build a multiple sequence alignment Edit and publish alignments Visualize protein 3-D structures Construct phylogenetic trees This up-to-date second edition includes newly created and popular databases and Internet programs as well as multiple new genomes. It provides tips for using servers and places to seek resources to find out about what's going on in the bioinformatics world. Bioinformatics for Dummies will show you how to get the most out of your PC and the right Web tools so you'll be searching databases and analyzing sequences like a pro!

Introduction

(1)

What This Book Does for You

(1)

Foolish Assumptions

(1)

How This Book Is Organized

(2)

Part I: Getting Started in Bioinformatics

(1)

Part II: A Survival Guide to Bioinformatics

(1)

Part III: Becoming a Pro in Sequence Analysis

(1)

Part IV: Becoming a Specialist: Advanced Bioinformatics Techniques

(1)

Part V: The Part of Tens

(1)

Icons Used in This Book

(1)

Where to Go from Here

(3)

Part I: Getting Started in Bioinformatics

(60)

Finding Out What Bioinformatics Can Do for You

(20)

What Is Bioinformatics?

(1)

Analyzing Protein Sequences

(7)

A brief history of sequence analysis

(1)

Reading protein sequences from N to C

(1)

Working with protein 3-D structures

(2)

Protein bioinformatics covered in this book

(1)

Analyzing DNA Sequences

(4)

Reading DNA sequences the right way

(1)

The two sides of a DNA sequence

(2)

Palindromes in DNA sequences

(1)

Analyzing RNA Sequences

(2)

RNA structures: Playing with sticky strands

(1)

More on nucleic acid nomenclature

(1)

DNA Coding Regions: Pretending to Work with Protein Sequences

(3)

Turning DNA into proteins: The genetic code

(1)

More with coding DNA sequences

(1)

DNA/RNA bioinformatics covered in this book

(1)

Working with Entire Genomes

(3)

Genomics: Getting all the genes at once

(1)

Genome bioinformatics covered in this book

(1)

How Most People Use Bioinformatics

(38)

Becoming an Instant Expert with PubMed/Medline

(13)

Finding out about a protein by its name

(2)

Searching PubMed using author's names

(3)

Searching PubMed using fields

(3)

Searching PubMed using limits

(3)

A few more tips about PubMed

(1)

Retrieving Protein Sequences

(9)

ExPASy: A prime Internet site for protein information

(3)

More advanced ways to retrieve protein sequences

(3)

Retrieving a list of related protein sequences

(3)

Retrieving DNA Sequences

(6)

Not all DNA is coding for protein

(1)

Going from protein sequences to DNA sequences

(1)

Retrieving the DNA sequence relevant to my protein

(4)

Using BLAST to Compare My Protein Sequence to Other Protein Sequences

(5)

Making a Multiple Protein Sequence Alignment with ClustalW

(5)

Part II: A Survival Guide to Bioinformatics

(130)

Using Nucleotide Sequence Databases

(36)

Reading into Genes and Genomes

(3)

Prokaryotes: Small bugs, simple genes

(2)

Eukaryotes: Bigger bugs, complex genes

(1)

Making Use (and Sense) of GenBank

(13)

Making sense of the GenBank entry of a prokaryotic gene

(5)

Making sense of the GenBank entry of an eukaryotic mRNA

(1)

Making sense of a GenBank eukaryotic genomic entry

(5)

Working with related GenBank entries

(1)

Retrieving GenBank entries without accession numbers

(1)

Using a Gene-Centric Database

(2)

Working with Whole-Genome Databases

(9)

Working with complete viral genomes

(3)

Working with complete bacterial genomes

(2)

More bacterial genomics at TIGR

(2)

Microbes from the environment at DoE

(1)

Exploring the Human Genome

(8)

Finding out about the Ensembl project

(7)

Using Protein and Specialized Sequence Databases

105

(24)

From Translated ORFs to Mature Proteins

107

(3)

ORFs: What you see is NOT what you get

107

(2)

A personal final destination for each protein

109

(1)

A combinatorial diversity of folds and functions

109

(1)

Reading a Swiss-Prot Entry

110

(13)

Deciphering the EGFR Swiss-Prot entry

110

(1)

General information about the entry

111

(1)

Name and origin of the protein

112

(2)

The References

114

(1)

The Comments

114

(2)

The Cross-References

116

(2)

The Keywords

118

(1)

The Features

119

(4)

Finally, the sequence itself

123

(1)

Finding Out More about Your Protein

123

(6)

Finding out more about ``modified amino acids

124

(1)

Some advanced biochemistry sites

125

(1)

Finding out more about biochemical pathways

125

(1)

Finding out more about protein structures

126

(1)

Finding out more about major protein families

127

(2)

Working with a Single DNA Sequence

129

(30)

Catching Errors Before It's Too Late

130

(4)

Removing vector sequences

130

(3)

Cases when you shouldn't discard your sequence

133

(1)

Computing/Verifying a Restriction Map

134

(1)

Designing PCR Primers

135

(3)

Analyzing DNA Composition

138

(7)

Establishing the G+C content of your sequence

138

(1)

Counting words in DNA sequences

139

(1)

Counting long words in DNA sequences

140

(2)

Experimenting with other DNA composition analyses

142

(1)

Finding internal repeats in your sequence

142

(3)

Identifying genome-specific repeats in your sequence

145

(1)

Finding Protein-Coding Regions

145

(8)

ORFing your DNA sequence

146

(2)

Analyzing your DNA sequence with GeneMark

148

(1)

Finding internal exons in vertebrate genomic sequences

149

(2)

Complete gene parsing for eukaryotic genomes

151

(1)

Analyzing your sequence with GenomeScan

151

(2)

Assembling Sequence Fragments

153

(4)

Managing large sequencing projects with public software

154

(1)

Assembling your sequences with CAP3

155

(2)

Beyond This Chapter

157

(2)

Working with a Single Protein Sequence

159

(38)

Doing Biochemistry on a Computer

160

(6)

Predicting the main physico-chemical properties of a protein

161

(3)

Interpreting ProtParam results

164

(2)

Digesting a protein in a computer

166

(1)

Doing Primary Structure Analysis

166

(8)

Looking for transmembrane segments

168

(6)

Looking for coiled-coil regions

174

(1)

Predicting Post-Translational Modifications in Your Protein

174

(6)

Looking for PROSITE patterns

175

(2)

Interpreting ScanProsite results

177

(3)

Finding Known Domains in Your Protein

180

(14)

Choosing the right collection of domains

182

(1)

Finding domains with InterProScan

183

(2)

Interpreting InterProScan results

185

(2)

Finding domains with the CD server

187

(2)

Interpreting and understanding CD server results

189

(1)

Finding domains with Motif Scan

190

(4)

Discovering New Domains in Your Proteins

194

(1)

More Protein Analysis for Free over the Internet

194

(3)

Part III: Becoming a Pro in Sequence Analysis

197

(130)

Similarity Searches on Sequence Databases

199

(36)

Understanding the Importance of Similarity

200

(1)

The Most Popular Data-Mining Tool Ever: Blast

201

(18)

Blasting protein sequences

201

(8)

Understanding your Blast output

209

(7)

Blasting DNA sequences

216

(2)

The Blast way of doing things

218

(1)

Controlling Blast: Choosing the Right Parameters

219

(7)

Controlling the sequence masking

220

(3)

Changing the Blast alignment parameters

223

(1)

Controlling the Blast output

224

(2)

Making Blast Iterative with PSI-Blast

226

(5)

PSI-Blasting protein sequences

226

(2)

Avoiding mistakes when running PSI-Blast

228

(2)

Discovering and using protein domains with Blast and PSI-Blast

230

(1)

Similarity Searches for Free over the Internet

231

(4)

Comparing Two Sequences

235

(30)

Making Sure You Have the Right Sequences and the Right Methods

236

(3)

Choosing the right sequences

236

(1)

Choosing the right method

237

(2)

Making a Dot Plot

239

(15)

Choosing the right dot-plot flavor

240

(1)

Using Dotlet over the Internet

241

(8)

Doing biological analysis with a dot plot

249

(5)

Making Local Alignments over the Internet

254

(7)

Choosing the right local-alignment flavor

255

(1)

Using Lalign to find the ten best local alignments

256

(2)

Interpreting the Lalign output

258

(3)

Making Global Alignments over the Internet

261

(1)

Using Lalign to Make a Global Alignment

262

(1)

Aligning Proteins and DNA

262

(1)

Free Pairwise Sequence Comparisons over the Internet

262

(3)

Building a Multiple Sequence Alignment

265

(38)

Finding Out if a Multiple Sequence Alignment Can Help You

266

(4)

Identifying situations where multiple alignments do not help

267

(1)

Helping your research with multiple sequence alignments

267

(3)

Choosing the Right Sequences

270

(11)

The kinds of sequences you're looking for

271

(4)

Gathering your sequences with online Blast servers

275

(6)

Choosing the Right Method of Multiple Sequence Alignment

281

(10)

Using ClustalW

282

(5)

Aligning sequences and structures with Tcoffee

287

(4)

Crunching large datasets with MUSCLE

291

(1)

Interpreting Your Multiple Sequence Alignment

291

(6)

Recognizing the good parts in a protein alignment

292

(2)

Taking your multiple alignment further

294

(3)

Comparing Sequences That You Can't Align

297

(2)

Making multiple local alignments with the Gibbs sampler

298

(1)

Searching conserved patterns

299

(1)

Internet Resources for Doing Multiple Sequence Comparisons

299

(4)

Making multiple alignments with ClustalW around the clock

300

(1)

Finding your favorite alignment method

300

(1)

Searching for motifs or patterns

301

(2)

Editing and Publishing Alignments

303

(24)

Getting Your Multiple Alignment in the Right Format

305

(8)

Recognizing the main formats

307

(1)

Working with the right format

307

(2)

Converting formats

309

(3)

Watching out for lost data

312

(1)

Using Jalview to Edit Your Multiple Alignment Online

313

(6)

Starting Jalview

314

(2)

Editing a group of sequences

316

(2)

Useful features of Jalview

318

(1)

Saving your alignment in Jalview

318

(1)

Preparing Your Multiple Alignment for Publication

319

(4)

Using Boxshade

319

(3)

Logos

322

(1)

Editing and Analyzing Multiple Sequence Alignments for Free over the Internet

323

(4)

Finding multiple-sequence-alignment editors

323

(1)

Finding tools to interpret your multiple sequence alignment

324

(1)

Finding tools for beautifying your multiple alignments

325

(2)

Part IV: Becoming a Specialist: Advanced Bioinformatics Techniques

327

(76)

Working with Protein 3-D Structures

329

(24)

From Primary to Secondary Structures

330

(6)

Predicting the secondary structure of a protein sequence

330

(4)

Predicting additional structural features

334

(2)

From the Primary Structure to the 3-D Structure

336

(14)

Retrieving and displaying a 3-D structure from a PDB site

337

(3)

Guessing the 3-D structure of your protein

340

(3)

Looking at sequence features in 3-D

343

(7)

Beyond This Chapter

350

(3)

Finding proteins with similar shapes

350

(1)

Finding other PDB viewers

350

(1)

Classifying your PDB structure

351

(1)

Doing homology modeling

351

(1)

Folding proteins in a computer

351

(1)

Threading sequences onto PDB structures

351

(1)

Looking at structures in movement

352

(1)

Predicting interactions

352

(1)

Working with RNA

353

(18)

Predicting, Modeling and Drawing RNA Secondary Structures

354

(1)

Using Mfold

355

(7)

Interpreting mfold results

359

(2)

Forcing interaction in mfold

361

(1)

Searching Databases and Genomes for RNA Sequences

362

(5)

Finding tRNAs in a genome

363

(1)

Using PatScan to look for RNA patterns

363

(4)

Finding the ``New'' RNAs: miRNAs and siRNAs

367

(1)

Doing RNA Analysis for Free over the Internet

368

(3)

Studying evolution with ribosomal RNA

369

(1)

Finding the small, non-coding RNA you need

369

(1)

Generic RNA resources

370

(1)

Building Phylogenetic Trees

371

(32)

Finding Out What Phylogenetic Trees Can Do for You

372

(1)

Preparing Your Phylogenetic Data

373

(10)

Choosing the right sequences for the right tree

374

(6)

Preparing your multiple sequence alignment

380

(3)

Building the Kind of Tree You Need

383

(17)

Computing your tree

383

(15)

Knowing what's what in your tree

398

(1)

Displaying your phylogenetic tree

399

(1)

Doing Phylogeny for Free over the Internet

400

(3)

Finding online resources

400

(1)

Finding generic resources

401

(1)

Collections of orthologous genes

402

(1)

Part V: The Part of Tens

403

(14)

The Ten (Okay, Twelve) Commandments for Using Servers

405

(6)

Keep in Mind: Your Data Is Never Secure on the Web

406

(1)

Remember the Server, the Database, and the Program Version You Used

406

(1)

Write Down the Sequence-Identification Numbers

407

(1)

Write Down the Program Parameters

407

(1)

Save Your Internet Results the Right Way

407

(1)

Use E-Values

408

(1)

Make Sure You Can Trust Your Alignments

408

(1)

Use Different Programs to Check Borderline Results

409

(1)

Stay Away from Unpublished Methods!

409

(1)

Databases Are Not Like Good Wine

409

(1)

Just Because It Looks Free Doesn't Mean It Is Free

410

(1)

Biting the Bullet at the Right Time

410

(1)

Some Useful Bioinformatics Resources

411

(6)

Ten Major Databases

411

(1)

Ten Major Bioinformatics Software Programs

412

(2)

Ten Major Resource Locators

414

(1)

Some Places to Find Out What's Really Going On

415

(2)

Index

417

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Bioinformatics For Dummies

Summary

Author Biography

Table of Contents

Supplemental Materials