Lecture 3

Dna Replication: 

• Bacterial genomes; 
• Directionality in DNA strands; 
• Replication origin (oriC); 
• Clump finding (LT)-clump; 
• DNA replication is asymetric; 
• Forward; 
• Skew diagram; 
• DnaA boxes;
• Hamming distance between 2 k-mers; 

K-mer and Pattern: 

• Count(Text, Pattern); 
• Approximate Patterns Matching; 

Regular Expressions (RES or Regex): 

• Flexivel Patterns; 
• Python: 
  • package RE
  • Function to find occurences; 
  • Overlaps; 
  • Sequence validation; 

Protein Motif: 

• Motifs; 
• Syntax rules; 
• Protein Motifs with RES