Genomics

  1. Bioinformatics and Computational Genomics
    1. Genomic Data Management
      1. Data Formats and Standards
        1. Sequence Formats
          1. FASTA Format
            1. FASTQ Format
              1. Quality Scores
              2. Alignment Formats
                1. SAM Format
                  1. BAM Format
                    1. CRAM Format
                    2. Variant Formats
                      1. VCF Format
                        1. BCF Format
                        2. Annotation Formats
                          1. GFF/GTF Formats
                            1. BED Format
                          2. Data Storage and Infrastructure
                            1. File Compression and Indexing
                              1. Database Systems
                                1. Cloud Computing Solutions
                                  1. Data Sharing Standards
                                    1. FAIR Data Principles
                                    2. Quality Control and Preprocessing
                                      1. Raw Data Quality Assessment
                                        1. Adapter and Contaminant Removal
                                          1. Quality Trimming
                                            1. Error Correction Methods
                                          2. Sequence Analysis and Alignment
                                            1. Pairwise Sequence Alignment
                                              1. Global Alignment Algorithms
                                                1. Needleman-Wunsch Algorithm
                                                2. Local Alignment Algorithms
                                                  1. Smith-Waterman Algorithm
                                                  2. Scoring Matrices
                                                    1. Substitution Matrices
                                                      1. Gap Penalties
                                                    2. Database Searching
                                                      1. BLAST (Basic Local Alignment Search Tool)
                                                        1. BLAST Algorithm
                                                          1. Types of BLAST Searches
                                                            1. Statistical Significance
                                                              1. Interpreting BLAST Results
                                                              2. BLAT (BLAST-Like Alignment Tool)
                                                                1. Specialized Search Tools
                                                                2. Multiple Sequence Alignment
                                                                  1. Progressive Alignment Methods
                                                                    1. ClustalW and ClustalOmega
                                                                      1. MUSCLE
                                                                        1. MAFFT
                                                                        2. Iterative Alignment Methods
                                                                          1. Profile-Based Methods
                                                                            1. Alignment Quality Assessment
                                                                          2. Genome Annotation
                                                                            1. Structural Annotation
                                                                              1. Gene Prediction Methods
                                                                                1. Ab Initio Gene Prediction
                                                                                  1. Hidden Markov Models
                                                                                    1. Neural Networks
                                                                                      1. Support Vector Machines
                                                                                      2. Evidence-Based Gene Prediction
                                                                                        1. EST and cDNA Evidence
                                                                                          1. RNA-Seq Evidence
                                                                                            1. Protein Homology
                                                                                            2. Comparative Gene Prediction
                                                                                            3. Non-Coding RNA Prediction
                                                                                              1. Repeat Element Annotation
                                                                                              2. Functional Annotation
                                                                                                1. Protein Function Prediction
                                                                                                  1. Homology-Based Annotation
                                                                                                    1. Domain-Based Annotation
                                                                                                      1. Structure-Based Annotation
                                                                                                      2. Gene Ontology (GO) Annotation
                                                                                                        1. Biological Process
                                                                                                          1. Molecular Function
                                                                                                            1. Cellular Component
                                                                                                              1. GO Evidence Codes
                                                                                                              2. Pathway Annotation
                                                                                                                1. KEGG Pathways
                                                                                                                  1. Reactome Pathways
                                                                                                                    1. BioCyc Pathways
                                                                                                                  2. Annotation Pipelines and Tools
                                                                                                                    1. Automated Annotation Systems
                                                                                                                      1. Manual Curation Processes
                                                                                                                        1. Community Annotation Projects
                                                                                                                      2. Major Genomic Databases and Resources
                                                                                                                        1. Primary Sequence Databases
                                                                                                                          1. NCBI GenBank
                                                                                                                            1. Database Structure
                                                                                                                              1. Sequence Submission
                                                                                                                                1. Data Retrieval
                                                                                                                                2. EMBL-EBI European Nucleotide Archive
                                                                                                                                  1. DDBJ DNA Data Bank of Japan
                                                                                                                                  2. Genome Browsers and Portals
                                                                                                                                    1. UCSC Genome Browser
                                                                                                                                      1. Track System
                                                                                                                                        1. Custom Track Creation
                                                                                                                                          1. Comparative Genomics Tools
                                                                                                                                          2. Ensembl Genome Browser
                                                                                                                                            1. Gene Annotation
                                                                                                                                              1. Comparative Genomics
                                                                                                                                                1. Variation Data
                                                                                                                                                2. NCBI Genome Data Viewer
                                                                                                                                                3. Specialized Databases
                                                                                                                                                  1. Protein Databases
                                                                                                                                                    1. Variation Databases
                                                                                                                                                      1. Expression Databases
                                                                                                                                                        1. Pathway Databases

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                                                                                                                                                    2. Genomic Technologies and Methodologies

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                                                                                                                                                    4. Structural and Functional Genomics