rtools

Bioinformatics Web Server for RNA

Enter your RNA sequence (single FASTA format, <= 400nt)
Samples: Hammerhead ribozyme, tRNA, H/ACA snoRNA, TPP-riboswitch

Softwares

Prediction of RNA secondary structure.

	: specify the inference engine
	: weight of base pairs

Prediction of RNA secondary structure by using homologous sequences.

	: specify the inference engine for secondary structure
	: specify the inference engine for pairwise alignment
	: weight of base pairs
	: E-value for homology search against Rfam
	: number of homologous sequences

Prediction of RNA pseudoknot based on maximizing expected accuracy.

	: specify the inference engine
	(NUPACK can be selected only when RNA length is <= 100nt)
	: weight of base pairs (level 2)

Calculation of energy changes of RNA secondary structures after base mutations.

: maximal span of base pairs

Calculation of probabilities that each RNA base position is located
within each secondary structural context.

: maximal span of base pairs

Calculation of of structural accessibility of RNA transcripts.

: maximal span of base pairs

Validation of RNA secondary structure.
structure.1

predicted by CentroidFold
: weight of base pairs
Your structure (dot-bracket format without sequence)

structure.2

predicted by RNAfold
Your structure (dot-bracket format without sequence)

Capturing alternative secondary structures of RNA.

	: specify the inference engine for canonical structure
	: weight of base pairs