* Biology Meets Programming: Bioinformatics for Beginners

** Week 1  
  
*** DNA replication

**** Origin of replication (ori)
    
     Locating an ori is key for gene therapy (e.g. viral vectors), to introduce a theraupetic gene.
     
**** Exercises: computational approaches to find ori in Vibrio Cholerae
     
***** Exercise: find Pattern
     
     We'll look for the *DnaA box* sequence, using a sliding window, in that case we will use the function [[./Code/Replication.py][Replication]] to find out how many times
     does a sequence appear in the genome.
     
     For the second part, we're going to calculate the frequency map of the sequences of length /k/, for that purpose we'll use [[./Code/FrequentWords.py][FrequentWords]] 
     
***** Exercise: Find the reverse complement of a sequence
     
      We're going to generate the reverse complement of a sequence, which is the complement of a sequence, read in the same direction (5' -> 3').
      In this case, we're going to use [[./Code/ReverseComplement.py][ReverseComplement]] 
      After using our function on the Vibrio's Cholerae genome, we realize that some of the frequent k-mers are reverse complements of other frequent ones.
     

*** Vocabulary
      - k-mer: subsquences of length /k/ in a biological sequence
      - Frequency map: sequence --> frequency of the sequence