Bioinformatics and Computational Biology

  1. Biological Databases and Data Management
    1. Major Public Databases
      1. Primary Sequence Databases
        1. NCBI GenBank
          1. Database Structure
            1. Accession Number System
              1. Data Submission Process
                1. Search and Retrieval
                2. European Nucleotide Archive
                  1. Data Organization
                    1. Integration with Other Resources
                    2. DNA Data Bank of Japan
                      1. Unique Features
                        1. Data Exchange
                      2. Protein Databases
                        1. UniProt Knowledge Base
                          1. Swiss-Prot Reviewed Entries
                            1. TrEMBL Unreviewed Entries
                              1. Protein Annotation Standards
                                1. Cross-References
                                2. Protein Data Bank
                                  1. Structure Deposition
                                    1. Data Validation
                                      1. Structure Retrieval
                                        1. Derived Databases
                                      2. Gene Expression Databases
                                        1. Gene Expression Omnibus
                                          1. Data Submission Standards
                                            1. Metadata Requirements
                                              1. Data Retrieval Methods
                                              2. ArrayExpress
                                                1. MIAME Standards
                                                  1. Data Processing Pipelines
                                                2. Functional Databases
                                                  1. Gene Ontology
                                                    1. Ontology Structure
                                                      1. Annotation Evidence Codes
                                                        1. Enrichment Analysis
                                                        2. KEGG Pathways
                                                          1. Pathway Maps
                                                            1. Ortholog Groups
                                                              1. Metabolic Networks
                                                              2. Reactome
                                                                1. Pathway Hierarchy
                                                                  1. Reaction Networks
                                                                    1. Cross-Species Comparison
                                                                  2. Specialized Databases
                                                                    1. Model Organism Databases
                                                                      1. FlyBase
                                                                        1. WormBase
                                                                          1. Mouse Genome Database
                                                                          2. Disease Databases
                                                                            1. OMIM
                                                                              1. ClinVar
                                                                                1. COSMIC
                                                                            2. Data Formats and Standards
                                                                              1. Sequence Data Formats
                                                                                1. FASTA Format
                                                                                  1. Header Line Structure
                                                                                    1. Sequence Representation
                                                                                      1. Variations and Extensions
                                                                                      2. FASTQ Format
                                                                                        1. Quality Score Encoding
                                                                                          1. Phred Scores
                                                                                            1. Format Variations
                                                                                            2. GenBank Format
                                                                                              1. Feature Tables
                                                                                                1. Annotation Standards
                                                                                              2. Alignment Formats
                                                                                                1. SAM Format
                                                                                                  1. Header Section
                                                                                                    1. Alignment Records
                                                                                                      1. Flag Field Interpretation
                                                                                                      2. BAM Format
                                                                                                        1. Binary Compression
                                                                                                          1. Indexing Methods
                                                                                                            1. Random Access
                                                                                                            2. CRAM Format
                                                                                                              1. Reference-Based Compression
                                                                                                                1. Lossless and Lossy Modes
                                                                                                              2. Structural Data Formats
                                                                                                                1. PDB Format
                                                                                                                  1. Coordinate Records
                                                                                                                    1. Header Information
                                                                                                                      1. Connectivity Data
                                                                                                                      2. mmCIF Format
                                                                                                                        1. Structured Data Representation
                                                                                                                          1. Extensibility
                                                                                                                          2. Structure Validation
                                                                                                                          3. Annotation Formats
                                                                                                                            1. GFF3 Format
                                                                                                                              1. Feature Hierarchy
                                                                                                                                1. Attribute Specification
                                                                                                                                2. GTF Format
                                                                                                                                  1. Gene Model Representation
                                                                                                                                    1. Transcript Structure
                                                                                                                                    2. BED Format
                                                                                                                                      1. Coordinate Systems
                                                                                                                                        1. Track Definition
                                                                                                                                      2. Variant Data Formats
                                                                                                                                        1. VCF Format
                                                                                                                                          1. Header Specifications
                                                                                                                                            1. Variant Records
                                                                                                                                              1. Genotype Information
                                                                                                                                              2. BCF Format
                                                                                                                                                1. Binary Representation
                                                                                                                                                  1. Indexing and Querying
                                                                                                                                              3. Data Quality and Validation
                                                                                                                                                1. Quality Control Metrics
                                                                                                                                                  1. Sequence Quality Assessment
                                                                                                                                                    1. Contamination Detection
                                                                                                                                                      1. Completeness Evaluation
                                                                                                                                                      2. Data Validation Procedures
                                                                                                                                                        1. Format Compliance
                                                                                                                                                          1. Biological Consistency
                                                                                                                                                            1. Cross-Reference Validation
                                                                                                                                                            2. Error Detection and Correction
                                                                                                                                                              1. Common Error Types
                                                                                                                                                                1. Automated Correction Methods
                                                                                                                                                                  1. Manual Curation Processes

                                                                                                                                                              Previous

                                                                                                                                                              2. Foundational Concepts and Skills

                                                                                                                                                              Go to top

                                                                                                                                                              Next

                                                                                                                                                              4. Sequence Analysis Methods