ARMADiLLO Output

ARMADiLLO produces multiple outputs including a list of number of mutations which is printed to the standard out. Each unique name of the antibodies analyzed produces a set of files. The set of files depends on which flag is used to indicate output. The list of flags with example files for the CH01 bNAB are shown:

  • -simple_text
    • CH01.ARMADiLLO.fasta
  • -text
    • CH01.ARMADiLLO.fasta
    • CH01.ARMADiLLO.Detailed.text
    • CH01.freq_table.txt
  • -HTML
    • CH01.ARMADiLLO.html
    • CH01.freq_table.html
    • CH01.tiles.html
  • -fulloutput
    • CH01.ARMADiLLO.fasta
    • CH01.ARMADiLLO.Detailed.text
    • CH01.freq_table.txt
    • CH01.ARMADiLLO.html
    • CH01.freq_table.html
    • CH01.tiles.html

Results Files

CH01.ARMADiLLO.html
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 (using a simple numbering scheme starting at 1 at the first residue). The third row is the nucleotide sequence. Below each base in this row is the mutability score 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 highlighted 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.
_images/CH01.table.png
CH01.tiles.html
The Overview tab displays an amino acid alignment of the sequence of interest aligned to the inferred UCA (inferred automatically by the program Cloanalyst ). Mutations are colored by their probability according to the legend below the alignment. A PDF or image of this view can be downloaded by clicking on the “Download PDF/PNG” icons at the bottom of the page.
_images/CH01.screenshot.png
CH01.freq_table.html
partial frequency table
_images/CH01.freqTable.png
CH01.ARMADiLLO.fasta

This is a text version of the tiles HTML file. The text file is similar to a fasta file containing the first line is the antibody name, second name is the UCA, the third is the antibody sequence, and the fourth is indicating mutations. The categories of probabilities identified by the number with the probability range corresponding to the number shown in the table below:

>CH01
EVQLVESGGGVVRPGGSLRLSCAASGFTFDDYGMSWVRQAPGKGLEWVSGINWNGGSTGYADSVKGRFTISRDNAKNSLYLQMNSLRAEDTALYHCARGTDYTIDDAGIHYYGSGTYWYFDLWGRGTLVTVSS
EVQLVESGANVVRPGGSLRLSCKASGFIFENFGFSWVRQAPGKGLQWVAGLNWNGGDTRYADSVKGRFRMSRDNSRNFVYLDMDKVGVDDTAFYYCARGTDYTIDDAGIHYQGSGTFWYFDLWGRGTLVSVSS
--------24------------4----2-221-4-----------3--3-1-----3-2---------42----32-23--4-253212---1-2----------------4----2------------2---

Table below shows the values found in the ARMADiLLO.fasta file which correspond to probability ranges:

X - 1 2 3 4 5 6
indel no mutation >10% 10%-2% 2%-1% 1%-0.1% 0.1%-0.01% <0.01%
CH01.ARMADiLLO.Detailed.txt

Detailed text file containing information similar to the data found in the <name>.ARMADiLLO.html file. Below is a portion of the CH01.ARMADiLLO.Detailed.txt:

sequence name:       CH01
markup header:       CH01|IGHV3-20*01|IGHD3-10*01|IGHJ2*01

pos  UCA AA  UCA NT  seq AA  seq NT          P(NT)   P(AA)
0    E       G       E       G               N/A     0.693
1            A               A               N/A
2            G               G               0.993
3    V       G       V       G               1.869   0.740
4            T               T               1.064
5            G               T       *       0.320
6    Q       C       Q       C               0.792   0.750
7            A               A               1.049
8            G               G               2.214
9    L       C       L       C               3.089   0.741
10           T               T               0.308
11           G               G               0.304
12   V       G       V       G               0.987   0.725
13           T               T               0.784
14           G               G               0.599
15   E       G       E       G               0.406   0.777
16           A               A               0.891
17           G               G               0.456
18   S       T       S       T               0.353   0.894
19           C               C               0.216
20           T               T               0.475
21   G       G       G       G               0.180   0.937
CH01.freq_table.txt

This text file containing the frequency table that is identical to the <name>.freq_table.html file. Below is a portion of the CH01.freq_table.txt file as an example:

pos,A,C,D,E,F,G,H,I,K,L,M,N,P,Q,R,S,T,V,W,Y
1,0.046026,0.000109,0.054888,0.692587,0.000102,0.046116,0.002774,0.000376,0.04222,0.004152,0.002404,0.003095,0.002883,0.043106,0.005473,0.001668,0.00289,0.045995,0.001375,0.001761
2,0.039752,0.000105,0.001162,0.029505,0.002204,0.026113,5.7e-05,0.019598,0.003511,0.068141,0.05775,0.000223,0.001677,0.000902,0.002998,0.001303,0.005039,0.739662,0.000286,1.2e-05
3,0.00052,0.000295,0.001778,0.009705,0.00023,0.000777,0.100629,0.000558,0.043009,0.023889,0.000785,0.007063,0.017885,0.749523,0.036306,0.001211,0.00173,0.000734,0.002155,0.001218
4,0.005967,7.9e-05,0.000128,0.003383,0.004667,0.002746,0.000281,0.005609,0.003495,0.74079,0.054421,0.000138,0.022387,0.007966,0.010551,0.007812,0.004093,0.123653,0.00181,2.4e-05
5,0.049846,7e-06,0.001734,0.034422,0.000482,0.029925,4.8e-05,0.010574,0.00287,0.068665,0.064194,8.5e-05,0.002003,0.000783,0.002501,0.001101,0.005371,0.725208,0.000172,9e-06
6,0.045533,1.3e-05,0.028818,0.777286,1.8e-05,0.064965,0.001012,0.000129,0.035438,0.001617,0.001855,0.001247,0.001431,0.014608,0.002706,0.000526,0.003117,0.019375,0.000168,0.000138
7,0.015214,0.016725,0.000158,1.1e-05,0.0169,0.000367,0.000314,0.000354,5e-06,0.001932,1.5e-05,0.000234,0.034619,1.3e-05,0.000611,0.894044,0.012548,0.00041,0.000418,0.005108
8,0.004763,9e-05,0.000849,0.020644,4e-06,0.937063,1.6e-05,2.4e-05,0.000569,0.000323,0.000183,2.1e-05,0.000151,0.00037,0.022485,0.000273,0.00034,0.005244,0.006577,1.1e-05
9,0.023785,0.000111,0.00259,0.067305,2.5e-05,0.684705,0.000152,0.002306,0.005354,0.001983,0.000159,0.000294,0.001659,0.001073,0.170454,0.021486,0.008058,0.008393,8.7e-05,2.1e-05
10,0.033872,0.026353,0.066866,0.009225,0.00099,0.708193,0.003698,0.002701,0.000438,0.001442,3.6e-05,0.006936,0.005062,0.000218,0.034596,0.069495,0.008695,0.019157,0.000308,0.001719
11,0.036335,3.9e-05,0.001563,0.027254,0.001818,0.024736,5.2e-05,0.007692,0.001469,0.096155,0.031858,9e-05,0.001998,0.00097,0.002466,0.001758,0.003098,0.759726,0.000903,2e-05
12,0.06637,7.4e-05,0.008767,0.105961,0.004292,0.066928,0.000354,0.123754,0.014916,0.138731,0.012939,0.001347,0.01009,0.004029,0.015095,0.005556,0.020502,0.400189,5.7e-05,4.9e-05
13,0.000327,0.003646,3.4e-05,0.000743,4.3e-05,0.051235,0.00096,1.9e-05,0.000499,0.004769,0.000317,1.7e-05,0.00611,0.010093,0.807677,0.0019,0.000338,0.000336,0.110877,6e-05
14,0.007415,0.000255,5.7e-05,2e-05,0.000271,0.000107,0.006102,0.000187,8e-06,0.016516,8e-06,0.000103,0.933412,0.000631,0.013233,0.01211,0.009221,0.000264,1.8e-05,6.2e-05
15,0.003675,6.8e-05,0.000483,0.016696,4e-06,0.944095,1.1e-05,1.3e-05,0.000409,0.000251,0.000179,1.5e-05,0.000112,0.000308,0.022632,0.000242,0.000256,0.004183,0.006364,4e-06
16,0.012839,0.000121,0.002129,0.049045,5e-06,0.888193,6.8e-05,0.000101,0.002773,0.000612,0.000711,0.000136,0.000588,0.001367,0.022944,0.000618,0.00105,0.012591,0.004096,1.3e-05
17,0.017927,0.021411,0.000689,2.4e-05,0.01949,0.000487,0.000889,0.000489,6.6e-05,0.003052,2.6e-05,0.001049,0.041783,1.9e-05,0.000626,0.871477,0.008914,0.000662,0.000517,0.010403
18,0.000421,1.3e-05,1.3e-05,0.000281,0.001165,0.000219,0.000646,0.000517,0.000219,0.909542,0.006267,5e-06,0.033152,0.017986,0.015097,0.000559,0.00047,0.013217,0.000205,6e-06
19,0.00052,0.000143,8.7e-05,0.001066,1.2e-05,0.042885,4.6e-05,0.004404,0.014997,0.000218,0.000382,0.001109,0.000395,0.00044,0.90871,0.013309,0.010852,0.00024,0.000182,3e-06

HTML Style Files

These style files are required for proper viewing of the HTML files in a web browser. ARMADiLLO will automatically create these files in the same directory as the HTML files. If the file HTML files are moved then these style files should be copied as well.

  • AMA.css
  • sequence_color.css