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Out-of-frame notation
Out-Of-Frame BLAST notation
When protein aligned to the nucleotide there are 6 possibilities of
match at any point. In OOF alignment - upper sequence is DNAP - 3-frame
translated DNA. Lower sequence is protein. At any position next protein
base may be aligned to 6 possible bases in DNAP:
(TBO - traditional blast output)
0: 3 nucleotides missing - gap (TBO notation "-")
OOF alignment with DNAP:
DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGG-GVLCV
| | | | | | | | | | | | | | | | |
D G T K F A T G G Q G Q D S G K V V
TBO:
DGTKFATGGQGQDSG-VV
DGTKFATGGQGQDSG VV
DGTKFATGGQGQDSGKVV
1: 2 nucleotides missing - "frameshift -2" (TBO notation "\\")
OOF alignment with DNAP:
DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGGGVLCV
| | | | | | | | | | | | | | |/ | |
D G T K F A T G G Q G Q D S GK V V
TBO:
DGTKFATGGQGQDSG\\GVV
DGTKFATGGQGQDSG VV
DGTKFATGGQGQDSG KVV
2: 1 nucletide missing - "frameshift -1" (TBO notation "\")
OOF alignment with DNAP:
DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGERGV
| | | | | | | | | | | | | | / | |
D G T K F A T G G Q G Q D S G K V
TBO:
DGTKFATGGQGQDS\GEV
DGTKFATGGQGQDS G V
DGTKFATGGQGQDS GKV
3: Complete match
OOF alignment with DNAP:
DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGEKRGV
| | | | | | | | | | | | | | | | |
D G T K F A T G G Q G Q D S G K V
TBO:
DGTKFATGGQGQDSGKV
DGTKFATGGQGQDSGKV
DGTKFATGGQGQDSGKV
4: 1 nucleotide insertion - "frameshift +1" (TBO notation "/")
OOF alignment with DNAP:
DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLWGGVEKRGV
| | | | | | | | | | | | | | | \
D G T K F A T G G Q G Q D S G K V
TBO:
DGTKFATGGQGQDSG/KV
DGTKFATGGQGQDSG KV
DGTKFATGGQGQDSG KV
5: 2 nucleotides insertion - "frameshift +2" (TBP notation "//")
OOF alignment with DNAP:
DTRGGDTPQKSVFSRAQNTLWGERGDTQKRGGAQRGDIFSLFLWGGEKRGV
| | | | | | | | | | | | | | \ | |
D G T K F A T G G Q G Q D S G K V
TBO:
DGTKFATGGQGQDS//GKV
DGTKFATGGQGQDS GKV
DGTKFATGGQGQDS GKV
Additional BLAST information is available from NCBI
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