Bioinformatics and Computational Biology

  1. Sequence Analysis Methods
    1. Pairwise Sequence Alignment
      1. Global Alignment Algorithms
        1. Needleman-Wunsch Algorithm
          1. Dynamic Programming Matrix
            1. Traceback Procedure
              1. Time and Space Complexity
                1. Implementation Considerations
              2. Local Alignment Algorithms
                1. Smith-Waterman Algorithm
                  1. Local Similarity Detection
                    1. Optimal Local Alignments
                      1. Multiple Local Alignments
                    2. Scoring Systems
                      1. Substitution Matrices
                        1. PAM Matrices
                          1. Construction Methodology
                            1. Evolutionary Distance
                              1. Matrix Selection
                              2. BLOSUM Matrices
                                1. Block-Based Construction
                                  1. Identity Thresholds
                                    1. Performance Characteristics
                                  2. Gap Penalty Models
                                    1. Linear Gap Penalties
                                      1. Affine Gap Penalties
                                        1. Position-Specific Penalties
                                      2. Alignment Statistics
                                        1. Statistical Significance
                                          1. Extreme Value Distribution
                                            1. E-values and p-values
                                          2. Database Similarity Searching
                                            1. Heuristic Search Methods
                                              1. Seed-and-Extend Strategies
                                                1. Speed vs Sensitivity Trade-offs
                                                  1. Index-Based Searching
                                                  2. BLAST Algorithm Family
                                                    1. BLAST Algorithm Principles
                                                      1. Word Finding
                                                        1. Extension Phase
                                                          1. Statistical Evaluation
                                                          2. BLAST Variants
                                                            1. BLASTn for Nucleotide Sequences
                                                              1. BLASTp for Protein Sequences
                                                                1. BLASTx for Translated Searches
                                                                  1. tBLASTn for Protein vs Translated Database
                                                                    1. tBLASTx for Translated vs Translated
                                                                    2. BLAST Parameters
                                                                      1. Word Size Selection
                                                                        1. Scoring Matrix Choice
                                                                          1. Gap Penalty Settings
                                                                            1. E-value Thresholds
                                                                            2. Result Interpretation
                                                                              1. High-Scoring Pairs
                                                                                1. Bit Scores
                                                                                  1. Query Coverage
                                                                                    1. Identity and Similarity
                                                                                  2. Alternative Search Methods
                                                                                    1. FASTA Algorithm
                                                                                      1. PSI-BLAST for Profile Searches
                                                                                        1. HMMER for HMM-Based Searches
                                                                                      2. Multiple Sequence Alignment
                                                                                        1. Progressive Alignment Methods
                                                                                          1. ClustalW Algorithm
                                                                                            1. Pairwise Alignment Phase
                                                                                              1. Guide Tree Construction
                                                                                                1. Progressive Alignment
                                                                                                2. MUSCLE Algorithm
                                                                                                  1. Iterative Refinement
                                                                                                    1. Anchor-Based Alignment
                                                                                                    2. T-Coffee Algorithm
                                                                                                      1. Consistency-Based Scoring
                                                                                                        1. Library Integration
                                                                                                      2. Iterative Methods
                                                                                                        1. MAFFT Algorithm
                                                                                                          1. Fast Fourier Transform
                                                                                                            1. Iterative Refinement
                                                                                                              1. Accuracy vs Speed Options
                                                                                                            2. Profile-Based Methods
                                                                                                              1. Hidden Markov Models
                                                                                                                1. Position-Specific Scoring
                                                                                                                2. MSA Quality Assessment
                                                                                                                  1. Alignment Accuracy Metrics
                                                                                                                    1. Conservation Scoring
                                                                                                                      1. Gap Distribution Analysis
                                                                                                                      2. MSA Visualization and Editing
                                                                                                                        1. Alignment Viewers
                                                                                                                          1. Manual Curation Techniques
                                                                                                                            1. Consensus Sequence Generation
                                                                                                                          2. Sequence Pattern Discovery
                                                                                                                            1. Regular Expression Patterns
                                                                                                                              1. Pattern Syntax
                                                                                                                                1. Biological Motif Representation
                                                                                                                                  1. Pattern Matching Algorithms
                                                                                                                                  2. Statistical Motif Discovery
                                                                                                                                    1. Position Weight Matrices
                                                                                                                                      1. Matrix Construction
                                                                                                                                        1. Scoring and Thresholds
                                                                                                                                          1. Background Models
                                                                                                                                          2. Expectation-Maximization Algorithms
                                                                                                                                            1. MEME Algorithm
                                                                                                                                              1. Gibbs Sampling
                                                                                                                                            2. Hidden Markov Models
                                                                                                                                              1. HMM Architecture
                                                                                                                                                1. States and Transitions
                                                                                                                                                  1. Emission Probabilities
                                                                                                                                                  2. Profile HMMs
                                                                                                                                                    1. Multiple Alignment Representation
                                                                                                                                                      1. Sequence Classification
                                                                                                                                                        1. Domain Detection
                                                                                                                                                        2. HMM Training
                                                                                                                                                          1. Baum-Welch Algorithm
                                                                                                                                                            1. Parameter Estimation
                                                                                                                                                          2. Functional Site Prediction
                                                                                                                                                            1. Active Site Identification
                                                                                                                                                              1. Binding Site Prediction
                                                                                                                                                                1. Signal Peptide Detection

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                                                                                                                                                            5. Genomics and Genome Analysis