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Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
The ViennaRNA Package is software, a set of standalone programs and libraries used for predicting and analysing RNA nucleic acid secondary structures. [1] The source code for the package is released as free and open-source software and compiled binaries are available for the operating systems Linux, macOS, and Windows.
In bioinformatics, Stemloc is an open source software for multiple RNA sequence alignment and RNA structure prediction based on probabilistic models of RNA structure known as Pair stochastic context-free grammars (also probabilistic context-free grammars). Stemloc attempts to simultaneously predict and align the structure of RNA sequences with ...
Sfold is a software program developed to predict probable RNA secondary structures through structure ensemble sampling and centroid predictions [1] [2] with a focus on assessment of RNA target accessibility, [3] for major applications to the rational design of siRNAs [4] in the suppression of gene expressions, and to the identification of targets for regulatory RNAs particularly microRNAs.
RNA-Skim RNA-Skim: a rapid method for RNA-Seq quantification at transcript-level. rSeq rSeq is a set of tools for RNA-Seq data analysis. It consists of programs that deal with many aspects of RNA-Seq data analysis, such as read quality assessment, reference sequence generation, sequence mapping, gene and isoform expressions (RPKMs) estimation, etc.
List of gene prediction software; List of disorder prediction software; List of Protein subcellular localization prediction tools; List of phylogenetics software; List of phylogenetic tree visualization software; Category:Metagenomics_software; Structural biology software. List of molecular graphics systems; List of protein-ligand docking ...
psRobot is a web-based tool for plant small RNA meta-analysis. psRobot computes stem-loop small RNA prediction, which aligns user uploaded sequences to the selected genome, extracts their predicted precursors, and predicts whether the precursors can fold into stem-loop shaped secondary structure. psRobot also computes small RNA target ...
Molecular design software; Molecule editor; Quantum chemistry computer programs; List of molecular graphics systems; List of protein structure prediction software; List of sequence alignment software; List of gene prediction software; List of RNA structure prediction software; Comparison of software for molecular mechanics modeling