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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.
Automated software package to annotate eukaryotic genes from RNA-Seq data and associated protein sequences Eukaryotes [1] FragGeneScan: Predicting genes in complete genomes and sequencing Reads: Prokaryotes, Metagenomes [2] ATGpr: Identifies translational initiation sites in cDNA sequences: Human [3] Prodigal
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
Software platform, allows organizations to integrate, analyze, and share complex biomedical data Linux, macOS, Windows: Apache: LabKey Software Foundation LAMMPS: Molecular dynamics program written in C++: Linux, macOS, Windows: Apache: Sandia National Laboratories. mothur: Software for analysis of 16S rRNA gene amplicon sequence data Linux ...
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 ...
Subjunc [44] is a specialized version of Subread. It uses all mappable regions in an RNA-seq read to discover exons and exon-exon junctions. It uses the donor/receptor signals to find the exact splicing locations. Subjunc yields full alignments for every RNA-seq read including exon-spanning reads, in addition to the discovered exon-exon junctions.
Rna22 is a pattern-based algorithm for the discovery of microRNA target sites and the corresponding heteroduplexes. [1]The algorithm is conceptually distinct from other methods for predicting microRNA:mRNA heteroduplexes in that it does not use experimentally validated heteroduplexes for training, instead relying only on the sequences of known mature miRNAs that are found in the public databases.