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?

Simple simulation
     Make up random sequences. Count how many times a regulatory sequence arises.
Pattern recognition
     Scan entire genome, counting sequences that satisfy criteria for regulatory sequence.

Regulation over gene expression
DNA-binding proteins
Nonrandom nature of biological DNA

Programs

Simple simulation: Dice roll (DiceRoll.pl)
     A model program just to get across the idea of a simulation.
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)
Arrays and loops (html) (Questions)
Implementing a simulation (html) (Questions)