PETcofold web server : Example data set

This example illustrates the usage of an Rfam seed alignment for predicting the RNA-RNA interaction in vertebrates between snoRNA mgU6-77 and U6 snRNA presented in Seemann SE et.al., Bioinformatics, 2010.
An example of two customized alignments, you will find here.

Input

RNA alignment

The Rfam seed alignment of the snRNA U6 can be chosen from the drop down list in the input form. The alignment of the snoRNA mgU6-77 was fetched from snoRNABase and its species names (identifier) were adapted using the drop down list of U6 identifiers: mgU6-77.fasta.

>Homo_sapiens_human
GCUCU---GUGAUGGAG-CCCAUGCGUGUCAUCUGAGCCUCUGGCUU-CCCUGCCAGU---GC---AG--CCCUG--GCAGUGUCCUACUUCCCAGGGCUGUUGUCU-GCCUGGCGGGAAG-----GUCCUGGGCAAA-GGAUCAGUCUUUGUACUCUGAGAGCAGACUA
>Pan_troglodytes_chimpanzee
GCUCU---GUGAUGGAG-CCCAUGCGUGUCAUCUGAGCCUCUGGCUU-CCCUGCCAGU---GC---AG--CCCUG--GCAGUGUCCUACUUCCCAGGGCUGUUGUCU-GCCUGGCGGGAAG-----GUCCUGGGCAAA-GGAUCAGUCUUUGUACUCUGAGAGCAGACUA
>Mus_musculus_house_mouse
GCUCU---GUGAUGAAC-CCCAUGCGUGUCAUCUGAG--CCUGGCUU-CCCUGUUGUU---ACCUUAG--CCCAG--GUAGUGUUCUACUUACCAGGGCUUUUGCCUGGCUUAUCAGGGAA-----GCUUUGGGCAAA-GGAUCAGUCCUUGUAUUCUGAGAGCAGAC-A
>Bos_taurus_cattle
GCUCU---GUGAUGAAC-UCCAUGCGUGUCAUCUGAG--CCUGGCUU-CCCUGUCAUC---UC---AG--CCCAG--GUAGUGUUCUACUUCCCAAGGCUGUUGUCUGGCCUGGAAAGGGG-----AUCCCAGGCAAA-GGAUCAACCUUUGUAUUCUGAGAGCAGAA-G
>Echinops_telfairi_small_Madagascar_hedgehog
GCUCU---GUGAUGAAC-CCCAUGCGUGUCAUCUGAG--CCCAGAUU-CCCUGUUGUC---UC---AG--CCCUGGUGUGGUGUUCUACUUCCCAGAGCUGUUGUCUGACCCAGUAGGAG--------UCUGGACAAAGGGAUCUAUCUUUCCAUUCUGAGAGCAGACGA
>Canis_lupus_familiaris_dog
GCUCU---GUGAUGAGC--CCAUGCGUGUCAUCUGAG--CCUGGCUU-CCCCGUC--C---UC---AG-CCCCGG--GGAGUGUUCUACUUCCCUGGCCUGUCAGCUGGCCUCGUGUGGGA-----GUCUU-GGCAAA-GGAUCAGCCUUCGUAUCCUGAGAGCAGAU-C
>Monodelphis_domestica_gray_short-tailed_opossum
GCUCU---GUGAUGAUCCCCCAUGCGUGUCAUCUGAG--CUCAGCUUCCCCUGAUCUC---UC---AGUUCCAAG--UGGGUGUUUUGCCCUCUGG------UCUCUGGGCUGGCAGUGG------CUUCUGGGCACA-UGAUCAUAAUUUA-ACCCUGAGAGCAAAUUG

Note that the identifiers in both alignments must be the same.

Options

The option Constraint stems get extended by inner and outer base pairs was chosen.

Output

The output shows the calculated phylogenetic tree, the PETcofold plain text output including the predicted joint RNA secondary structure, score and relative score, an image of the sequence conservation in the joint RNA multiple alignment, and a dotplot of base pair and single stranded reliabilities calculated by the PETcofold scoring scheme:

Input

RNA alignment

Options

Output

Joint phylogenetic tree

PETcofold output

1st step - intra-molecular folding using PETfold

2nd step - inter-molecular cofolding

Predicted consensus joint RNA secondary structure

Dotplot of PETcofold reliabilities of base pairs and single stranded positions