💻 Bioinformatics & Computational Biology: One Night Revision & Cram Sheet
Teach a biology student to interpret sequence and structure data, and the algorithms that compare them, well enough to use a result and to say when it does not support the sentence written under it.
🌟 Core Axioms & High-Yield Golden Rules
8 Core PrinciplesNon-negotiable foundational truths frequently tested in direct conceptual and numerical exam questions. Click checkbox to mark as mastered.
What the field is: Key focus includes Bioinformatics and computational biology, why sequences exist, genomes, transcriptomes, proteomes, structures. Understand fundamental structures, metabolic pathways, and regulatory feedback loops.
💡 Chapter 1 Priority FocusDatabases and file formats: Key focus includes Primary and derived archives, RefSeq, UniProt. Understand fundamental structures, metabolic pathways, and regulatory feedback loops.
💡 Chapter 2 Priority FocusPairwise alignment: Key focus includes Homology, similarity, identity, global and local alignment, dynamic programming. Understand fundamental structures, metabolic pathways, and regulatory feedback loops.
💡 Chapter 3 Priority FocusScoring and database search: Key focus includes PAM and BLOSUM, BLAST seeds, E-value and bit score. Understand fundamental structures, metabolic pathways, and regulatory feedback loops.
💡 Chapter 4 Priority FocusMultiple alignment and motifs: Key focus includes Progressive alignment, iterative and consistency methods, patterns, profiles, profile HMMs. Understand fundamental structures, metabolic pathways, and regulatory feedback loops.
💡 Chapter 5 Priority FocusMolecular phylogenetics: Key focus includes Distance, parsimony, likelihood, Bayesian trees, support, long-branch attraction. Understand fundamental structures, metabolic pathways, and regulatory feedback loops.
💡 Chapter 6 Priority FocusGenome sequencing and annotation: Key focus includes Shotgun assembly, repeats, long reads and Hi-C. Understand fundamental structures, metabolic pathways, and regulatory feedback loops.
💡 Chapter 7 Priority FocusTranscriptomics and variation: Key focus includes Microarrays and RNA-seq, normalisation, differential expression. Understand fundamental structures, metabolic pathways, and regulatory feedback loops.
💡 Chapter 8 Priority Focus📚 Chapter-by-Chapter Rapid Cram Breakdown
10 ModulesHigh-density review of every curriculum chapter. Click any chapter title to view full in-depth lecture notes.
What the field is →
- Master Bioinformatics and computational biology: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master why sequences exist: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master genomes, transcriptomes, proteomes, structures: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Primary and derived archives: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master RefSeq: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master UniProt: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master PDB: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Gene Ontology: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
Pairwise alignment →
- Master Homology, similarity, identity: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master global and local alignment: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master dynamic programming: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master affine gaps: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master PAM and BLOSUM: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master BLAST seeds: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master E-value and bit score: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master low-complexity sequence: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Progressive alignment: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master iterative and consistency methods: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master patterns, profiles, profile HMMs: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master logos: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Distance, parsimony, likelihood, Bayesian trees: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master support: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master long-branch attraction: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master clocks: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master orthology: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Shotgun assembly: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master repeats: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master long reads and Hi-C: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master coverage: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master gene finding: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Microarrays and RNA-seq: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master normalisation: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master differential expression: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master variant calls: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master GWAS: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
Protein bioinformatics →
- Master Composition and hydrophobicity: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master secondary structure: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master homology modelling: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master AlphaFold: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master docking: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master Versions and database dates: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master circular validation: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master multiple testing: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master base rates: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
- Master criticising a hit: understand underlying structural mechanisms, biochemical pathways, and diagnostic indicators.
⚖️ Must-Know Comparison & Distinction Tables
1 TablesSide-by-side matrices comparing commonly confused biological mechanisms, kinetic types, and pathways.
Key Comparative Distinctions in Bioinformatics & Computational Biology
| Conceptual Feature | Type A / Classical Model | Type B / Advanced Model | Significance in Exams |
|---|---|---|---|
| Structural Basis | Primary baseline configuration | Modified / adaptive architecture | Distinguishes specialized physiological adaptations |
| Kinetic / Regulatory Control | Constitutive / basal expression | Inducible / allosteric modulation | Crucial for feedback homeostasis questions |
| Experimental Verification | In vitro biochemical assay | In vivo genetic knock-down / tagging | Commonly tested in research methodology questions |
⚠️ Examiner Traps & Common Student Mistakes
2 PitfallsClassic trap questions designed by examiners to catch uncritical students. Don't lose easy marks here!
Overlooking Feedback Regulation in Bioinformatics & Computational Biology
Treating biological pathways as simple linear forward sequences.
Almost all physiological and molecular circuits operate via negative feedback, feed-forward loops, or reciprocal allosteric control.
Confusing In Vitro with In Vivo Phenotypes
Assuming enzyme or cellular behavior in isolated buffer mirrors complex in vivo conditions.
Cellular crowding, compartmentalization, and membrane microdomains significantly alter binding affinities and kinetic rates.
📐 Key Formulas & Numerical Constants
2 FormulasStandard Equilibrium Constant
Keq = [Products] / [Reactants]Determines direction of chemical/biological reactions at dynamic equilibrium.
Relative Quantitative Ratio
Ratio = Experimental_Value / Baseline_ControlStandardizes comparative fold-change in quantitative biological assays.
🏛️ Landmark Scientists & Nobel Discoveries
5 PioneersFrequently tested in historical milestone and match-the-following exam questions.
Frederick Sanger
🏅 Two Nobel Prizes in Chemistry: 1958 (Unshared, for determining the complete primary amino acid structure of insulin) and 1980 (Shared, for inventing dideoxy DNA sequencing)Major landmark discoveries
Carl Richard Woese
🏅 Crafoord Prize in Biosciences (2003, royal Swedish Academy of Sciences)Major landmark discoveries
Motoo Kimura
🏅 Crafoord Prize in Biosciences (1992)Major landmark discoveries
Margaret Oakley Dayhoff
Major landmark discoveries
Temple F. Smith & Michael S. Waterman
Major landmark discoveries
🎯 Rapid-Fire Active Recall Checklist
10 QuestionsTest your memory before stepping into the exam hall. Try to answer mentally, then tap "Reveal Answer" to verify!