RNA secondary structure prediction. 2' structure of RNA using M-Fold, mfold, bioinformatic tools online and software to predict RNA folding and hairpin loops.
Server which predicts conserved secondary structure elements of homologous RNAs. The input of a set of RNA sequences are not required to be previously aligned. - [Read more CARNAC]
Tool which aids in the design and quality control of small interfering RNAs (siRNAs) for RNA interference (RNAi) and gene silencing. It evaluates the inhibitory potency of potential siRNA sequences as well as identifying gene regions that have a high sil - [Read more DEQOR]
ERPIN (Easy RNA Profile IdentificatioN) takes as input an RNA sequence alignment and secondary structure annotation and will identify a wide variety of known RNA motifs (such as tRNAs, 5S rRNAs, SRP RNA, C/D box snoRNAs, hammerhead motifs, miRNAs and othe - [Read more ERPIN]
Server which provides iterated loop matching and maximum weighted matching algorithms for pseudoknot containing RNA secondary structure prediction. Algorithms can apply thermodynamic and comparative information, and thus can be used for either aligned or - [Read more ILM]
The Database of Macromolecular Movements (MolMovDB) contains a collection of animated protein and RNA structures to assist in the exploration of macromolecular flexibility. Software for structure analysis is also available. - [Read more MolMovDB]
MOLPROBITY is a structure analysis and validation program that can calculate and display steric, H-bonding, and van der Waals interactions for known structures of proteins, nucleic acids, and complexes. - [Read more MOLPROBITY]
A RNA secondary structure prediction program which implements two methods, one based on random stacking and the other based on helical region distributions. - [Read more RDfolder]
Server with three tools for the rational design of small interfering RNAs (Sirna), antisense oligonucleotides (Soligo), and trans-cleaving ribozymes (Sribo). A fourth tool, Srna, returns output including general folding features. - [Read more Sfold]
Server for computing small interfering RNA (siRNA) sequences which are best suited for mammalian RNA interference (RNAi). The site accepts a sequence as input and returns a list of siRNA candidates. - [Read more siDirect]
Server aiding the design of short interfering RNAs (siRNAs) by providing information on stability, SNPs and specificity of the a potential siRNA. - [Read more siRNA Selection Server]
This resource includes siSearch, AOSearch, and a siRNAdb which provides a platform for mining an siRNA database, and searching for non-specific matches to your siRNA (small interfering RNAs). - [Read more siRNAdb]
RNA secondary structure viewer applet; must be integrated into web page to be implemented; can link to multiple computational backends. - [Read more SStructView]
T7 RNAi Oligo Designer (TROD) aids in the design of DNA oligonucleotides for short interfering RNA (siRNA) synthesis with T7 RNA polymerase. It takes an input of a cDNA sequence and outputs a list of DNA oligos for ordering. - [Read more TROD]
Comprises a C code library and several stand-alone programs for the prediction and comparison of RNA secondary structures. - [Read more Vienna RNA Package]
