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