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Bioinformatics For Dummies

For Dummieserschienen am01.07.2011
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!


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,
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Produkt

KlappentextWere 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!


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,
Details
Weitere ISBN/GTIN9781118051108
ProduktartE-Book
EinbandartE-Book
FormatEPUB
Erscheinungsjahr2011
Erscheinungsdatum01.07.2011
Seiten464 Seiten
SpracheEnglisch
Dateigrösse19865
Artikel-Nr.3048738
Rubriken
Genre9201

Inhalt/Kritik

Inhaltsverzeichnis
Introduction.

Part I: Getting Started in Bioinformatics.

Chapter 1: Finding Out What Bioinformatics Can Do for You.

Chapter 2: How Most People Use Bioinformatics.

Part II: A Survival Guide to Bioinformatics.

Chapter 3: Using Nucleotide Sequence Databases.

Chapter 4: Using Protein and Specialized Sequence Databases.

Chapter 5: Working with a Single DNA Sequence.

Chapter 6: Working with a Single Protein Sequence.

Part III: Becoming a Pro in Sequence Analysis.

Chapter 7: Similarity Searches on Sequence Databases.

Chapter 8: Comparing Two Sequences.

Chapter 9: Building a Multiple Sequence Alignment.

Chapter 10: Editing and Publishing Alignments.

Part IV: Becoming a Specialist: Advanced Bioinformatics
Techniques.

Chapter 11: Working with Protein 3-D Structures.

Chapter 12: Working with RNA.

Chapter 13: Building Phylogenetic Trees.

Part V: The Part of Tens.

Chapter 14: The Ten (Okay, Twelve) Commandments for Using
Servers.

Chapter 15: Some Useful Bioinformatics Resources.

Index.
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Leseprobe

Contents


Title




Introduction



What This Book Does for You



Foolish Assumptions



How This Book Is Organized



Icons Used in This Book



Where to Go from Here





Part I : Getting Started in Bioinformatics




Chapter 1: Finding Out What Bioinformatics Can Do for You



What Is Bioinformatics?



Analyzing Protein Sequences



Analyzing DNA Sequences



Analyzing RNA Sequences



DNA Coding Regions: Pretending to Work with Protein Sequences



Working with Entire Genomes





Chapter 2: How Most People Use Bioinformatics



Becoming an Instant Expert with PubMed/Medline



Retrieving Protein Sequences



Retrieving DNA Sequences



Using BLAST to Compare My Protein Sequence to Other Protein Sequences



Making a Multiple Protein Sequence Alignment with ClustalW






Part II : A Survival Guide to Bioinformatics




Chapter 3: Using Nucleotide Sequence Databases



Reading into Genes and Genomes



Making Use (and Sense) of GenBank



Using a Gene-Centric Database



Working with Whole-Genome Databases



Exploring the Human Genome





Chapter 4: Using Protein and Specialized Sequence Databases



From Translated ORFs to Mature Proteins



Reading a Swiss-Prot Entry



Finding Out More about Your Protein





Chapter 5: Working with a Single DNA Sequence



Catching Errors Before It s Too Late



Computing/Verifying a Restriction Map



Designing PCR Primers



Analyzing DNA Composition



Finding Protein-Coding Regions



Assembling Sequence Fragments



Beyond This Chapter





Chapter 6: Working with a Single Protein Sequence



Doing Biochemistry on a Computer



Doing Primary Structure Analysis



Predicting Post-Translational Modifications in Your Protein



Finding Known Domains in Your Protein



Discovering New Domains in Your Proteins



More Protein Analysis for Free over the Internet






Part III : Becoming a Pro in Sequence Analysis




Chapter 7: Similarity Searches on Sequence Databases



Understanding the Importance of Similarity



The Most Popular Data-Mining Tool Ever: BLAST



Controlling BLAST: Choosing the Right Parameters



Making BLAST Iterative with PSI-BLAST



Similarity Searches for Free over the Internet





Chapter 8: Comparing Two Sequences



Making Sure You Have the Right Sequences and the Right Methods



Making a Dot Plot



Making Local Alignments over the Internet



Making Global Alignments over the Internet



Using Lalign to Make a Global Alignment



Aligning Proteins and DNA



Free Pairwise Sequence Comparisons over the Internet





...




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Autor

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.
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