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

Sergei Shavirin

Last modified: Tue Oct 17 10:56:56 EDT 2000