Scientific story (html)
In brief: You find by chance a sequence upstream from an interesting gene that looks suspiciously like a regulatory sequence. How can you assess the likelihood of your find?Bioinformatic tools
Simple simulationMolecular biology concepts
Make up random sequences. Count how many times a regulatory sequence arises.
Scan entire genome, counting sequences that satisfy criteria for regulatory sequence.
Regulation over gene expressionPerl focus: Loops and arrays
Nonrandom nature of biological DNA
Simple simulation: pre-Dice roll (pre-DiceRoll.pl)Notes
A model program just to get across the idea of a simulation... but one that's ridiculous
because it's written without any knowledge of loops or arrays.
Simple simulation: Dice roll (DiceRoll.pl)
A model program just to get across the idea of a simulation... a bit less ridiculous
as it uses loops (but not arrays)
Simple simulation/Pattern recognition: Sequence search through simulated genome
Explores notion of randomness. We will write this program by combining the strategy of DiceRoll
with the tools from FindMatches.
Pattern recognition: Sequence search through entire genome (FindMatches.pl)
For comparison with above
Data: Small sequence file for testing (AnabSeq.nt)
Data: Full sequence file for real thing (AnabaenaChromosome.nt)
Regulatory protein and their binding sites (PDF) (Questions)Problem Set - Molecular biology (PDF)
Arrays and loops (html) (Questions)
Implementing a simulation (html) (Questions)