Format the document in a consistent manner

Notebook.org

@@ -1,5 +1,7 @@
 * Biology Meets Programming: Bioinformatics for Beginners
+
 ** Week 1
+
 *** DNA replication
 
 **** Origin of replication (ori)
@@ -95,7 +97,6 @@ def PatternMatching(Pattern, Genome):
 We find out that the /9-mers/ with the highest frequency appear in cluster.
 There 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,
@@ -119,6 +120,7 @@ We have to try another computational approach,
 find clusters of /k-mers/ repeated in a small interval.
 
 ** Week 2
+
 *** DNA replication (II)
 
 **** Replication process
@@ -257,7 +259,6 @@ def SkewArray(Genome):
     return Skew
 #+END_SRC
 
-
 **** Finding /DnaA boxes/
      
 When we look for /DnaA boxes/ in the minimal skew region,
@@ -383,6 +384,7 @@ def Count(Motifs):
 ***** Exercise: Form the most frequent sequence of nucleotides
       
 Finally, we can form a Consensus string, to get a candidate regulatory motif:
+
 #+BEGIN_SRC python
 def Consensus(Motifs):
     consensus = ""
@@ -493,8 +495,7 @@ def Pr(Text, Profile):
     return probability
 #+END_SRC
 
-Now we're finally ready to assemble all the pieces and implement a Greedy Motif
-Search Algorithm:
+Now we're finally ready to assemble all the pieces and implement a Greedy Motif Search Algorithm:
 
 #+BEGIN_SRC python
 def GreedyMotifSearch(Dna, k, t):
@@ -583,9 +584,7 @@ def Pr(Text, Profile):
 
 ***** Motifs in tuberculosis
 
-Tuberculosis is an infectious disease, caused by a bacteria called /Mycobacterium
-tuberculosis/. The bacteria can stay latent in the host for decades, in hypoxic
-environments.
+Tuberculosis is an infectious disease, caused by a bacteria called /Mycobacterium tuberculosis/. The bacteria can stay latent in the host for decades, in hypoxic environments.
 Our Greedy Algorithm can help us identify a motif that might be involved
 in the process.