CentroidHomfold predicts RNA secondary structures by employing automatically collected homologous sequences of the target. Homologous sequences are collected from Rfam using LAST. If homologous sequences are available, CentroidHomfold can predict secondary structures for the target sequence more accurately than CentroidFold using homologous sequence information with the probabilistic consistency transformation for base-pairing probabilities.

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

Options

McCaskill(BL) McCaskill(Turner) CONTRAfold	: specify the inference engine for secondary structure
CONTRAlign ProbCons	: specify the inference engine for pairwise alignment
2^10 2^9 2^8 2^7 2^6 2^5 2^4 2^3 2^2 2^1 2^0 2^-1 2^-2 2^-3 2^-4 2^-5	: weight of base pairs
0.1 0.01 0.001 0.0001	: E-value for homology search against Rfam
10 20 30 40 50	: number of homologous sequences