Harvard:Biophysics 101/2007/02/22

Required feature set, Due Feb 27

• Your program should be able to recognize and report the following at a minimum
  • Determination of reading frame
  • 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

Reading frame determination

5'→3' frame 1: start codon position: 20. stop codon position: 155.  Transcript length: 135.  (**using this one**)
5'→3' frame 2: start codon position: 77. stop codon position: 82.  Transcript length: 5
5'→3' frame 3: start codon position: 33, 65. stop codon position: 12.  Transcript length: 0
3'→5' frame 1: start codon position: NA. stop codon position: 112.  Transcript length: NA
3'→5' frame 2: start codon position: 51. stop codon position: 77, 108.  Transcript length: 26 
3'→5' frame 3: start codon position: 37. stop codon position: 38.  Transcript length: 1

Nucleic acid point mutations

• Silent

Silent point mutation found: C367G. Amino acid result: ARG122ARG

• Non-silent with corresponding amino acid change)

Non-silent point mutation found: A547C. Amino acid 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)

• Similar to deletions

Optional: detailed reporting of significant amino acid changes (stop codon, ±cysteine, ±charged, hydrophobic ↔ hydrophilic, possible splice sites, etc.)

Frame shift deletion caused early termination.  Stop codon moved to amino acid position 25 (was 166).

Warning: non-silent mutation at amino acid position 22:  nonpolar residue (G) replaced with charged residue (D)