Here I present: Jean-Michael Claverie & Cedric Notredame, “Bioinformatics for Dummies”, 2011. This book consists of fifteen (15) chapters divided into four (4) parts. The “table of contents” of the book is shown BELOW.
Table of Contents
Introduction
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
Chapter 9: Building a Multiple Sequence Alignment Finding Out if a Multiple Sequence Alignment Can Help You Choosing the Right Sequences Choosing the Right Method of Multiple Sequence Alignment Interpreting Your Multiple Sequence Alignment Comparing Sequences That You Can’t Align Internet Resources for Doing Multiple Sequence Comparisons
Chapter 10: Editing and Publishing Alignments Getting Your Multiple Alignment in the Right Format Using Jalview to Edit Your Multiple Alignment Online Preparing Your Multiple Alignment for Publication Editing and Analyzing Multiple Sequence Alignments for Free over the Internet
Part IV: Becoming a Specialist: Advanced Bioinformatics Techniques.
Chapter 11: Working with Protein 3-D Structures from Primary to Secondary Structures from the Primary Structure to the 3-D Structure Beyond This Chapter
Chapter 12: Working with RNA Predicting, Modeling, and Drawing RNA Secondary Structures Using Mfold Searching Databases and Genomes for RNA Sequences Finding the “New” RNAs: miRNAs and siRNAs Doing RNA Analysis for Free over the Internet
Chapter 13: Building Phylogenetic Trees Finding Out What Phylogenetic Trees Can Do for You Preparing Your Phylogenetic Data Building the Kind of Tree You Need Doing Phylogeny for Free over the Internet
Part V: The Part of Tens.
Chapter 14: The Ten (Okay, Twelve) Commandments for Using Servers Keep in Mind: Your Data Is Never Secure on the Web Remember the Server, the Database, and the Program Version You Used Write Down the Sequence-Identification Numbers Write Down the Program Parameters Save Your Internet Results the Right Way Use E-Values Make Sure You Can Trust Your Alignments Use Different Programs to Check Borderline Results Stay Away from Unpublished Methods! Databases Are Not Like Good Wine Just Because It Looks Free Doesn’t Mean It Is Free . . . Biting the Bullet at the Right Time
Chapter 15: Some Useful Bioinformatics
Here I presented: Jean-Michael Claverie & Cedric Notredame, “Bioinformatics for Dummies”, 2011.
COMMENTS
Most people need the “human linkage map”; and, Oak Ridge National Laboratory of the USA gives this poster for free (shown BELOW). Additionally, the online “Mendelian Inheritance in Man” with this book is all you need for bioinformatics.
