Galaxy |

RNAsnoop (version 2.1.6.0)

Select Filetype:

Query sequences:

Target sequences:

Maximal alignment length:

--alignmentLength

Calculate the stem structure subject to constraints:

--constraint

Maximal energy difference between the mfe and the desired suboptimal structure:

--energy-threshold

advanced options:

RNAsnoop

reads a target RNA sequence and a H/ACA snoRNA sequence from a target and query file, respectively and computes optimal and suboptimal secondary structures for their hybridization. The calculation can be done roughly done in O(nm), where is n the length of the target sequence and m is the length of the snoRNA stem, as it is specially tailored to the special case of H/ACA snoRNA. For general purpose target predictions, please have a look at RNAduplex, RNAup, RNAcofold and RNAplex.

Input format

RNAsnoop requires two input files

either two Fasta files
or two Clustal alignment files

Outputs

The computed optimal and suboptimal structure are given, one structure per line. Each line consist of: The structure in dot bracket format with a "&" separating the two strands. The '<>' brackets represent snoRNA intramolecular interactions, while the '()' brackets represent intermolecular interactions between the snoRNA and its target. The range of the structure in the two sequences in the format "from,to : from,to"; the energy of duplex structure in kcal/mol. If available the opening energy are also returned.