Mutation Frequencies

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

The following command in the GLUE console calculates the amino acid frequencies at a specific position within a feature of CHIKV alignment:

Mode path: /project/chikv
GLUE> alignment AL_CHIKV_ECSA amino-acid frequency -c -r REF_MASTER_CHIKV -f E1 -l 226 226

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

+=========+=======+===========+============+======================+
| feature | codon | aminoAcid | numMembers |      pctMembers      |
+=========+=======+===========+============+======================+
| E1      | 226   | A         | 3050       | 74.19119435660423    |
| E1      | 226   | L         | 1          | 0.024324981756263683 |
| E1      | 226   | V         | 1060       | 25.784480661639503   |
+=========+=======+===========+============+======================+

Command Breakdown

alignment AL_CHIKV_ECSA Selects the alignment for chikungunya virus (ECSA genotype).

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

-c Calculates the frequencies recursively, including any sub-alignments of AL_CHIKV_ECSA. In CHIKV-GLUE, alignments are arranged hierarchically to reflect evolutionary relationships.

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

-f E1 Indicates the coding feature within the reference sequence (E1) where amino acid frequencies will be calculated.

-l 226 226 Specifies the location within the feature to be analyzed. Here, it focuses on a single amino acid position (226).

Interpretation of the Output

• feature: The coding feature analyzed (in this case, envelope).
• codon: The codon position within the feature (position 226).
• 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.

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