Bioinformatics For Dummies

by Claverie, Jean-Michel; Notredame, Cedric

• ISBN13: 9780470089859
• ISBN10: 0470089857
• Edition: 2nd
• Format: Paperback
• Copyright: 2006-12-18
• Publisher: For Dummies

Summary

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!

Author Biography

Jean-Michel Claverie is Professor of Medical Bioinformatics at the School of Medicine of the Université de la Méditerranée, and a consultant in genomics and bioinformatics. He is the founder and current head of the Structural & Genomic Information Laboratory, located in Marseilles, a sunny city on the Mediterranean coast of France. Using science as a pretext to travel, Jean-Michel has held positions in Paris (France), Sherbrooke (PQ, Canada), the Salk Institute (La Jolla, CA), the Pasteur Institute (Paris), Incyte pharmaceutical (Palo Alto, CA); and the National Center for Biotechnology Information (Bethesda, MD). He has used computers in biology since the early days –– his Ph.D. work involved modeling biochemical reactions by programming an 8K Honeywell 516 computer right from the console switches! Although he has no clear recollection of it, he has been credited with introducing the French word “bioinformatique” in the late eighties, before involuntarily coining the catchy “bioinformatics” by mistranslating it while giving a talk in English!
Jean-Michel’s current research interests are in microbial and structural genomics, and in the development of bioinformatic methods for the prediction of gene function. He is the author or coauthor of more than 150 scientific publications, and a member of numerous international review panels and scientific councils. In his spare time, he enjoys the relaxed pace of life in Marseilles, with his wife Chantal and their two sons, Nicholas and Raphael.

Cedric Notredame is a researcher at the French National Centre for Scientific Research. Cedric has used and abused the facilities offered by science to wander around Europe. After a Ph.D. at EMBL (Heidelberg, Germany) and at the European Bioinformatics Institute (Cambridge, UK) under the supervision of Des Higgins (yes, the ClustalW guy), Cedric did a post-doc at the National Institute of Medical Research (London, UK), in the lab of Willie Taylor and under the supervision of Jaap Heringa. He then did a post-doc in Lausanne (Switzerland) with Phillip Bucher, and remained involved with the Swiss Institute of Bioinformatics for several years. Having had his share of rain, snow, and wind, Cedric has finally settled in Marseilles, where the sun and the sea are simply warmer than any other place he has lived in.
Cedric dedicates most of his research to the multiple sequence alignment problem and its many applications in biology. His friends claim that his entire life (past, present, future) is somehow stuffed into the T-Coffee multiple-sequence alignment package. When he is not busy dismantling T-Coffee and brewing new sequences, Cedric enjoys life in the company of his wife, Marita.

Table of Contents

Introduction	1	(1)
What This Book Does for You	1	(1)
Foolish Assumptions	2	(1)
How This Book Is Organized	2	(2)
Part I: Getting Started in Bioinformatics	3	(1)
Part II: A Survival Guide to Bioinformatics	3	(1)
Part III: Becoming a Pro in Sequence Analysis	3	(1)
Part IV: Becoming a Specialist: Advanced Bioinformatics Techniques	3	(1)
Part V: The Part of Tens	4	(1)
Icons Used in This Book	4	(1)
Where to Go from Here	4	(3)
Part I: Getting Started in Bioinformatics	7	(60)
Finding Out What Bioinformatics Can Do for You	9	(20)
What Is Bioinformatics?	9	(1)
Analyzing Protein Sequences	10	(7)
A brief history of sequence analysis	12	(1)
Reading protein sequences from N to C	13	(1)
Working with protein 3-D structures	14	(2)
Protein bioinformatics covered in this book	16	(1)
Analyzing DNA Sequences	17	(4)
Reading DNA sequences the right way	17	(1)
The two sides of a DNA sequence	18	(2)
Palindromes in DNA sequences	20	(1)
Analyzing RNA Sequences	21	(2)
RNA structures: Playing with sticky strands	22	(1)
More on nucleic acid nomenclature	23	(1)
DNA Coding Regions: Pretending to Work with Protein Sequences	23	(3)
Turning DNA into proteins: The genetic code	24	(1)
More with coding DNA sequences	25	(1)
DNA/RNA bioinformatics covered in this book	26	(1)
Working with Entire Genomes	26	(3)
Genomics: Getting all the genes at once	27	(1)
Genome bioinformatics covered in this book	28	(1)
How Most People Use Bioinformatics	29	(38)
Becoming an Instant Expert with PubMed/Medline	29	(13)
Finding out about a protein by its name	30	(2)
Searching PubMed using author's names	32	(3)
Searching PubMed using fields	35	(3)
Searching PubMed using limits	38	(3)
A few more tips about PubMed	41	(1)
Retrieving Protein Sequences	42	(9)
ExPASy: A prime Internet site for protein information	42	(3)
More advanced ways to retrieve protein sequences	45	(3)
Retrieving a list of related protein sequences	48	(3)
Retrieving DNA Sequences	51	(6)
Not all DNA is coding for protein	51	(1)
Going from protein sequences to DNA sequences	52	(1)
Retrieving the DNA sequence relevant to my protein	53	(4)
Using BLAST to Compare My Protein Sequence to Other Protein Sequences	57	(5)
Making a Multiple Protein Sequence Alignment with ClustalW	62	(5)
Part II: A Survival Guide to Bioinformatics	67	(130)
Using Nucleotide Sequence Databases	69	(36)
Reading into Genes and Genomes	70	(3)
Prokaryotes: Small bugs, simple genes	70	(2)
Eukaryotes: Bigger bugs, complex genes	72	(1)
Making Use (and Sense) of GenBank	73	(13)
Making sense of the GenBank entry of a prokaryotic gene	73	(5)
Making sense of the GenBank entry of an eukaryotic mRNA	78	(1)
Making sense of a GenBank eukaryotic genomic entry	79	(5)
Working with related GenBank entries	84	(1)
Retrieving GenBank entries without accession numbers	85	(1)
Using a Gene-Centric Database	86	(2)
Working with Whole-Genome Databases	88	(9)
Working with complete viral genomes	89	(3)
Working with complete bacterial genomes	92	(2)
More bacterial genomics at TIGR	94	(2)
Microbes from the environment at DoE	96	(1)
Exploring the Human Genome	97	(8)
Finding out about the Ensembl project	98	(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