Results of the Bayesian Phylogentic Footprint
Alignment of query and comparison sequence for HELP SAMPLE
The above example shows the detailed relationship between the two sequences. From this graph you can see that there are at least 3 major blocks conserved in the
query sequence (1-67,72-105,257-263) The data used to generate this plot is in "Probability Profile" File which can be viewed by clicking on the url near the bottom of this page.
Probability of residue conservation in query sequence for HELP SAMPLE
The above example graphs the probability of conservation of each residue in the query sequence. This is equivalent to collapsing the "Alignment of query and comparison sequence" graph along the data(comparison) axis. The data for this graph is in the "Marginal probability of the query sequence" file which can be viewed by clicking on the url near the bottom of this page.
Temperature plot of residue conservation in query sequence
> 1A human I1 ifn_gene_human v00536 and m32746 small
| 1 | 2 |
| G | TATGACTTTTTAATAGTACTTGTTTGTGGTTGAAAATGACTGAATATCGACTTGCTGT |
| 60 | 67 | 68 | 72 | 73 | 79 | 81 | 90 | 92 | 105 | 106 | 109 |
| AGCATCT | C | TGAT | A | GGCTGT | CA | TCTCTTGTA | GG | CAGTCATTTTGAG | A | TTT | GGTGTTATTT |
| 119 |
| TGTTAATTATTGACTAGATGAGTTCCTTGACTAAATAATCTAGATATTGTTTTAACCTT |
| 178 |
| CTGCTCAGTTTGTATAGAGACTTAAAAGGGATTTATGAATTTTCCAAAAGATGGGCATA |
| 237 | 256 | 257 | 263 | 264 |
| ATATGGGTATGAAGCATAA | T | GATGTT | A | ATAATTTTGTGGTGGGAACTCATTCAGTTGTG |
| 296 |
| ATAGTCAAGGAGTATGCAGATTGAAAAAAATGATTGGTTATTAGTTTTTGACTTCTCAG |
| 355 |
| ACTCTAAGGTCAAGATTAGCATTAAAAAGGTAATAGGAAATGTTTACAAATTAAAGTCA |
| 414 |
| AAAAGGTCCTTAAAGCTTTGGCTTAAAAAAATAACTGATAGGTGATTTTCTCCAAAAAG |
| 473 |
| TGATTTCAACATTCTGCTTCTCTATCTATATTACTTGTGAAGTATTCCGGAACTTCGTT |
Color Key for Probability of Conservation
| 0-0.199 |
0.2-0.399 |
0.4-0.599 |
0.6-0.799 |
0.8-0.999 |
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The above example show the probability of conservation of each residue in the query sequence. This is equivalent to collapsing "Alignment of query and comparison sequence" graph along the data(comparison) axis. This is the same as the "Probability of residue conservation in query sequence" graph but shown as a temperature plot instead. The color red means that the base is highly conserved and the color blue means it is poorly conserved. The data for this graph is in the "Marginal probability of the query sequence file" which can be viewed by clicking on the url near the bottom of this page.
The URLs above are the data files used to make the graphs and other important information.
The "Run file output" includes the various probabilities for the number of
conserved blocks. This example shows that probability that there are exactly
3 conserved blocks is 0.281207 and the probability that there are more than
3 conserved blocks is 0.633378.
The "Block alignment file" includes the most probable block alignments.
In this example it shows that the most probable conserved blocks are
(1-67) (72-105) and (256-263)
(see Bioinformatics 1998;14(1):25-39 for detail explanation of bayesian aligner)
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