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Foreword | |
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Preface | |
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Introduction | |
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Hello BLAST | |
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What Is BLAST? | |
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Using NCBI-BLAST | |
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Alternate Output Formats | |
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Alternate Alignment Views | |
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The Next Step | |
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Further Reading | |
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Theory | |
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Biological Sequences | |
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The Central Dogma of Molecular Biology | |
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Evolution | |
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Genomes and Genes | |
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Biological Sequences and Similarity | |
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Further Reading | |
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Sequence Alignment | |
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Global Alignment: Needleman-Wunsch | |
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Local Alignment: Smith-Waterman | |
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Dynamic Programming | |
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Algorithmic Complexity | |
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Global Versus Local | |
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Variations | |
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Final Thoughts | |
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Further Reading | |
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Sequence Similarity | |
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Introduction to Information Theory | |
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Amino Acid Similarity | |
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Scoring Matrices | |
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Target Frequencies, lambda, and H | |
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Sequence Similarity | |
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Karlin-Altschul Statistics | |
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Sum Statistics and Sum Scores | |
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Further Reading | |
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Practice | |
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BLAST | |
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The Five BLAST Programs | |
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The BLAST Algorithm | |
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Further Reading | |
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Anatomy of a BLAST Report | |
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Basic Structure | |
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Alignments | |
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A BLAST Statistics Tutorial | |
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Basic BLAST Statistics | |
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Using Statistics to Understand BLAST Results | |
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Where Did My Oligo Go? | |
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20 Tips to Improve Your BLAST Searches | |
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Don't Use the Default Parameters | |
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Treat BLAST Searches as Scientific Experiments | |
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Perform Controls, Especially in the Twilight Zone | |
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View BLAST Reports Graphically | |
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Use the Karlin-Altschul Equation to Design Experiments | |
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When Troubleshooting, Read the Footer First | |
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Know When to Use Complexity Filters | |
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Mask Repeats in Genomic DNA | |
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Segment Large Genomic Sequences | |
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Be Skeptical of Hypothetical Proteins | |
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Expect Contaminants in EST Databases | |
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Use Caution When Searching Raw Sequencing Reads | |
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Look for Stop Codons and Frame-Shifts to find Pseudo-Genes | |
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Consider Using Ungapped Alignment for BLASTX, TBLASTN, and TBLASTX | |
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Look for Gaps in Coverage as a Sign of Missed Exons | |
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Parse BLAST Reports with Bioperl | |
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Perform Pilot Experiments | |
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Examine Statistical Outliers | |
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Use links and topcomboN to Make Sense of Alignment Groups | |
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How to Lie with BLAST Statistics | |
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BLAST Protocols | |
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BLASTN Protocols | |
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BLASTP Protocols | |
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BLASTX Protocols | |
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TBLASTN Protocols | |
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TBLASTX Protocols | |
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Industrial-Strength BLAST | |
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Installation and Command-Line Tutorial | |
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NCBI-BLAST Installation | |
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WU-BLAST Installation | |
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Command-Line Tutorial | |
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Editing Scoring Matrices | |
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BLAST Databases | |
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FASTA Files | |
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BLAST Databases | |
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Sequence Databases | |
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Sequence Database Management Strategies | |
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Hardware and Software Optimizations | |
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The Persistence of Memory | |
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CPUs and Computer Architecture | |
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Compute Clusters | |
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Distributed Resource Management | |
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Software Tricks | |
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Optimized NCBI-BLAST | |
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BLAST Reference | |
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NCBI-BLAST Reference | |
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Usage Statements | |
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Command-Line Syntax | |
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blastall Parameters | |
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formatdb Parameters | |
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fastacmd Parameters | |
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megablast Parameters | |
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bl2seq Parameters | |
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blastpgp Parameters (PSI-BLAST and PHI-BLAST) | |
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blastclust Parameters | |
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WU-BLAST Reference | |
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Usage Statements | |
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Command-Line Syntax | |
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WU-BLAST Parameters | |
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xdformat Parameters | |
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xdget Parameters | |
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Appendixes | |
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NCBI Display Formats | |
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Nucleotide Scoring Schemes | |
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NCBI-BLAST Scoring Schemes | |
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blast-imager.pl | |
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blast2table.pl | |
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Glossary | |
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Index | |