25 lines
725 B
Org Mode
25 lines
725 B
Org Mode
* 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:
|
||
|
||
#+begin_src python
|
||
count = 0
|
||
for i in range(len(Text)-len(Pattern)+1):
|
||
if Text[i:i+len(Pattern)] == Pattern:
|
||
count = count+1
|
||
print(Pattern + ": " + count)
|
||
#+end_src
|
||
|
||
*** Vocabulary
|
||
- k-mer: subsquences of length /k/ in a biological sequence
|