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RNAtips
Predicts regions with high likelihood of temperature-induced structural changes. RNAtips is a web server which can be used to analyze the location of temperature-induced changes in the secondary structure of RNA and to compare such changes between two sequences of the same length. The software can be applied to a broad spectrum of research topics such as drug development, molecular diagnostic and disease prognosis, evolutionary mechanisms, ecology, investigation of climate change effects.
STOAT / Statistics Of Architectural Topology
Calculates statistical values of secondary structures. STOAT is a web application which calculates four statistical values from the secondary structure of folded RNA strings: the Shannon entropy, the Forbenius norm, the Base-pairing propensity and the mean stem length. The secondary structure of the various input sequences are obtained by interactions with the RNAfold program from the Vienna package. The software also translates sequences from FASTA to DCSE format.
MARTEN / Molecular Analysis and Recording Tool for Evolutionary Numeration
Counts the number of unpaired, paired and bulged nucleotides in folded RNA sequences. MARTEN is a web application which codes geometrical features in paired and unpaired regions of the molecules as linearly ordered multistate characters and produces an output for analysis with standard phylogenetic software. The software also translates the secondary structure of folded RNA sequences from the DCSE alignment format to the bracket notation.
NOBAI / Numeration of Objects in Biology: Alignment Inferences
Automates the task of coding information in the secondary structure of folded RNA sequences. NOBAI is a web server which consists of four separate modules, MARTEN, STOAT, STRINGGEN and OMROKGEN. The software codes topological and thermodynamic information related to the secondary structure of RNA molecules as multi-state phylogenetic characters, builds character matrices directly and provides sequence randomization options.
RNAscClust
Implements an algorithm to cluster a set of structured RNAs taking their respective structural conservation into account. For a set of multiple structural alignments of RNA sequences, each containing a paralog sequence included in a structural alignment of its orthologs, RNAscClust computes minimum free-energy structures for each sequence using conserved base pairs as prior information for the folding. The paralogs are then clustered using a graph kernel-based strategy, which identifies common structural features. The clustering accuracy clearly benefits from an increasing degree of compensatory base pair changes in the alignments.
lncLocator
Predicts long non-coding RNA (lncRNA) subcellular localization. lncLocator is an ensemble predictor that combines four learning machines using a stacked ensemble strategy. The learning machines are random forest with features extracted by deep neural networks (RFA), support vector machine with features extracted by deep neural networks (SVMA), random forest with raw kmer features (RFR) and support vector machine with raw k-mer features (SVMR), respectively. The software consists of three major steps: (1) feature representation, (2) prediction engine construction, and (3) stacked ensemble.
RNA-PAIRS / RNA Probabilistic Assignment of Imino Resonance Shifts
A method for the automated assignment of RNA imino resonances with synchronized verification and correction of predicted secondary structure. RNA-PAIRS represents an advance in modeling the assignment paradigm because it seeds the probabilistic network for assignment with experimental NMR data, and predicted RNA secondary structure, simultaneously and from the start. Subsequently, RNA-PAIRS sets in motion a dynamic network that reverberates between predictions and experimental evidence in order to reconcile and rectify resonance assignments and secondary structure information.
piRNA / Partition function for InteRacting Nucleic Acids
Obsolete
Computes joint and individual partition functions for two RNA sequences. piRNA is an efficient algorithm to calculate a partition function of two interacting nucleic acid strands. This method considers almost all physically possible secondary structures that do not contain pseudoknots, crossing interactions and ‘zigzag’s. It also estimates equilibrium concentrations of single and double joint species, ensemble energy, and melting temperatures.
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CRW / Comparative RNA Web
Disseminates comparative sequence and structure models and data. CRW is an online RNA sequence and structure information, the result of extensive analysis, interpretation, data collection, and a computer and web development program. The four major types of comparative information and systems available for the three ribosomal RNAs (5S, 16S, and 23S rRNA), transfer RNA (tRNA), and two of the catalytic intron RNAs (group I and group II) are: (i) Current Comparative Structure Models, (ii) Nucleotide Frequency and Conservation Information, (iii) Sequence and Structure Data and (iv) Data Access Systems.

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