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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.
Linux, macOS, Unix, Windows [4] GPL and LGPL: Collaborative project Galaxy: Scientific workflow and data integration system Unix-like: Academic Free: Collaborative project GenePattern: Scientific workflow system that provides access to hundreds of genomic analysis tools Unix-like (public server); Linux, macOS, Windows: MIT: Broad Institute, UC ...
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
Salmon is a software tool for computing transcript abundance from RNA-seq data using either an alignment-free (based directly on the raw reads) or an alignment-based (based on pre-computed alignments) approach. It uses an online stochastic optimization approach to maximize the likelihood of the transcript abundances under the observed data.
In that experiment, RosettaDock made a high-accuracy prediction for the docking between streptococcal pyogenic exotoxin A and a T cell-receptor β-chain, and a medium accuracy prediction for a complex between porcine α-amylase and a camelid antibody. While the RosettaDock method only made two acceptably accurate predictions out of seven ...
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 ...
Can use quality scores, intron lengths, and computation splice site predictions to perform and performs an unbiased alignment. Can be trained to the specifics of a RNA-seq experiment and genome. Useful for splice site/intron discovery and for gene model building. (See PALMapper for a faster version). Yes, client-server Free, GPL 2 RazerS