bioinformatics-course/Notebook.org

• Biology Meets Programming: Bioinformatics for Beginners
  • Week 1
    • DNA replication
      • Origin of replication (ori)
      • Exercise: computational approach to find ori in bacteria
    • Vocabulary

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.

Exercise: computational approach to find ori in bacteria

We'll look for the DnaA box sequence, using a sliding window, in that case our code would be the following:

  count = 0
  
for i in range(len(Text)-len(Pattern)+1):
    if Text[i:i+len(Pattern)] == Pattern:
      count = count+1 
  print(Pattern + ": " + count)

Vocabulary

• k-mer: subsquences of length k in a biological sequence