Processing

When ARMADiLLO is started, the page changes to the one shown below. This page shows the unique job ID along with the basic information associated with the run. This page should auto-refresh every 2 seconds and will display the results when they are available. If the page does not auto-refresh, use the job ID or job URL to check on the results manually.



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Results

ARMADiLLO generates two figures, accessible as tabs on the output page:

The Overview tab displays an amino acid alignment of the sequence of interest aligned to the UCA (inferred automatically by the program Cloanalyst or manually supplied). Mutations are colored by their probability according to the legend below the alignment. A PDF or PNG image of this view can be downloaded by clicking on the "Download PDF/PNG" icons at the bottom of the page.



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Results

ARMADiLLO generates two figures, accessible as tabs on the output page:

The Details tab displays a nucleotide level view of the input sequence aligned to the inferred UCA. The first three rows of each block comprises the UCA sequence. The next 3 rows comprise the input sequence and the last row is the probability of the amino acid observed at that position in the input sequence. The first row is the UCA amino acid sequence. The second row is the amino acid position number (first residue is 1). The third row is the nucleotide sequence. Below each base in this row is the mutability score, which represents the propensity for that base position to mutate, and is calculated using the S5F model. AID hot spots are highlighted in red (mutability score >2) and AID cold spots are highlighted in blue (mutability score <0.3). The fourth row is the amino acid sequence of the input sequence. Mutations are highlited in yellow. The fifth row is the amino acid position number of the input sequence. The sixth row is the nucleotide sequence of the input sequence with the mutability score listed below and hot spots and cold spots highlighted as in the third row. The seventh row is the estimated probability of the amino acid observed in the input sequence. Hovering over the probability in the 7th row will display the probabilities of all 20 amino acids for the position. A red arrow below the alignment displays any nucleotide changes that are the result of a mutation at an AID cold spot.



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