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

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