Mutation Frequencies

Dengue-GLUE can provide a detailed frequency distribution of amino acids at a specific position within a DENV coding feature, based on the alignments contained with the project. This can enable insights into the variability and conservation of DENV proteins.

The following command in the GLUE console calculates the amino acid frequencies at a specific position within a feature of a dengue virus type 2 (DENV2) alignment:

Mode path: /project/dengue
GLUE> alignment AL_DENV_2 amino-acid frequency -c -r REF_MASTER_DENV2 -f envelope -l 52 52

This command produces results in a tabular output format like this:

+==========+=======+===========+============+====================+
| feature  | codon | aminoAcid | numMembers |     pctMembers     |
+==========+=======+===========+============+====================+
| envelope | 52    | E         | 4          | 1.3840830449826989 |
| envelope | 52    | H         | 89         | 30.79584775086505  |
| envelope | 52    | K         | 1          | 0.3460207612456747 |
| envelope | 52    | Q         | 190        | 65.7439446366782   |
| envelope | 52    | Y         | 5          | 1.7301038062283738 |
+==========+=======+===========+============+====================+

Command Breakdown

alignment AL_DENV_2 Selects the alignment for dengue virus type 2 (DENV2).

amino-acid frequency Instructs GLUE to calculate amino acid frequencies within the selected alignment.

-c Calculates the frequencies recursively, including all sub-alignments of DENV2. In Dengue-GLUE, alignments are arranged hierarchically to reflect evolutionary relationships.

-r REF_MASTER_DENV2 Specifies the constraining reference sequence, REF_MASTER_DENV2, which defines the coordinate space and the wild type amino acid for comparison.

-f envelope Indicates the coding feature within the reference sequence (envelope) where amino acid frequencies will be calculated.

-l 52 52 Specifies the location within the feature to be analyzed. Here, it focuses on a single amino acid position (52).

Interpretation of the Output

• feature: The coding feature analyzed (in this case, envelope).
• codon: The codon position within the feature (position 52).
• aminoAcid: The amino acid found at the specified codon position.
• numMembers: The number of sequences in the alignment containing the specified amino acid at the given position.
• pctMembers: The percentage of sequences in the alignment containing the specified amino acid at the given position.