Harvard:Biophysics 101/2007/02/22
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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)