* 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.
     
**** 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 Cholerae's/ genome, we realize that some of the frequent k-mers are reverse complements of other frequent ones.
     
***** Exercise: Find a subsequence within a sequence
      
      We're going to find the ocurrences of a subsquence inside a sequence, and save the index of the first letter in the sequence.
      This time, we'll use [[./Code/PatternMatching.py][PatternMatching]] 
      After using our function on the /Vibrio Cholerae's/ genome, we find out that the /9-mers/ with the highest frequency appear in cluster.
      This is strong statistical evidence that our subsequences are /DnaA boxes/.

      
**** Computational approaches to find ori in any bacteria
     
     Now that we're pretty confident about the /DnaA boxes/ sequences that we found, we are going to check if they are a common pattern in the rest of bacterias.
     We're going to find the ocurrences of the sequences in /Thermotoga petrophila/ using [[./Code/Replication.py][Replication]]
     
     After the execution, we observe that there are *no* ocurrences of the sequences found in /Vibrio Cholerae/.
     We can conclude that different bacterias have different /DnaA boxes/.
     
     We have to try another computational approach then, find clusters of /k-mers/ repeated in a small interval.

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