This example illustrates the input and output of the PETfold web server.

Input

RNA alignment

The alignment in FASTA format looks like this, download the alignment file: example.fasta.

>gca_bovine
AGCCCUGUGGUGAAUUUACACGUUGAAUUGCAAAUUCAGAGAAGCAGCUUCAAU-UCUGCCGGGGCUU
>gca_chicken
GACUCUGUAGUGAAGU-UCAUAAUGAGUUGCAAACUCGUUGAUGUACACUAA-AGUGUGCCGGGGUCU
>gca_mouse
GGUCUUAAGGUGAUA-UUCAUGUCGAAUUGCAAAUUCGAAGGUGUAGAGAAAU-CUCUACUAAGACUU
>gca_rat
AGCCUUAAGGUGAUU-AUCAUGUCGAAUUGCAAAUUCGAAGGUGUAGAGAAUCU-UCUACUAAGGCUU

Phylogenetic tree (optional)

The phylogenetic tree in Newick format looks like this:

(gca_chicken:0.37262,(gca_rat:0.017848,gca_mouse:0.070927):0.290067,gca_bovine:0.15964):0.001;

Note that the names in the tree must match the names in the alignment file.

RNA secondary structure (optional)

The RNA secondary structure in dot-bracket format looks like this:

(((((((..(((......))).(((((((...)))))))....(((((.......)))))))))))).

Output

The output shows the input, phylogenetic tree, the PETfold plain text output including the predicted RNA secondary structure and score, images of the predicted consensus RNA secondary structure, and a dotplot of base pair and single stranded reliabilities calculated by the PETfold model:

Phylogenetic tree


Download PS | PDF | Newick format

PETfold output

Download this file

Predicted consensus RNA secondary structure


Download PS | PDF


Download PS | PDF

Dotplot of PETfold reliabilities of base pairs and single stranded positions


Download PS | PDF | dotplot file