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 &harr; 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 point mutation found: C367G. Amino acid result: ARG122ARG Non-silent point mutation found: A547C. Amino acid result: HIS182PRO Nucleic acid deletions 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 ATC CTG Prot Result:      G   I       L        (5'-3' frame 2) 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)
 * Silent
 * Non-silent with corresponding amino acid change)
 * frame shift (note there are 6 possible frames: three for 5'-3' plus three for 3'-5'
 * 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)
 * Similar to deletions

Optional: detailed reporting of significant amino acid changes (stop codon, ±cysteine, ±charged, hydrophobic &harr; 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)