Harvard:Biophysics 101/2007/02/22

Required feature set

• Your program should be able to recognize and report the following at a minimum
  • Nucleic acid point mutations (silent vs non-silent with corresponding amino acid change)
  • Nucleic acid deletions (frame shift vs non-frame shift, with amino acid position where change occurred)
  • Nucleic acid insertions (frame shift vs non-frame shift, with amino acid position where change occurred)
  • Detailed reporting of significant amino acid changes (stop codon, ±cysteine, ±charged, hydrophobic ↔ hydrophilic)

Example outputs

Nucleic acid point mutations

• Silent

Silent point mutation found: C367G.  Result: ARG122ARG

• Non-silent with corresponding amino acid change)

Non-silent point mutation found: A547C.  Result: HIS182PRO

Nucleic acid deletions

• frame shift (note there are 6 possible frames: three for 5'-3' plus three for 3'-5'

Frame shift deletion found: 4 base deletion, position 98 to 101.  
DNA Reference:    GGG ATT AAT CCT GCG
Prot Reference:    G   I   N   P   A    (5'-3' frame 2)
DNA Result:       GGG AT----C CTG
Prot Result:       G   I       L        (5'-3' frame 2)

• non-frame shift, with amino acid position where change occurred

Non-frame shift deletion found: 3 base deletion, position 99 to 101
DNA Reference:    GGG ATT AAT CCT GCG
Prot Reference:    G   I   N   P   A    (5'-3' frame 2)
DNA Result:       GGG ATT --- CCT GCG
Prot Result:       G   I       P   A    (5'-3' frame 2)

• Nucleic acid insertions (frame shift vs non-frame shift, with amino acid position where change occurred)
• Detailed reporting of significant amino acid changes (stop codon, ±cysteine, ±charged, hydrophobic ↔ hydrophilic)