Search Results for "rna structure"
Sort By:
Showing 27 open source projects for "rna structure"
View related business solutions-
Our Free Plans just got better! | Auth0You asked, we delivered! Auth0 is excited to expand our Free and Paid plans to include more options so you can focus on building, deploying, and scaling applications without having to worry about your security. Auth0 now, thank yourself later.
-
Gemini 3 and 200+ AI Models on One PlatformBuild generative AI apps with Vertex AI. Switch between models without switching platforms.
-
1
IsoQuant
Transcript discovery and quantification with long RNA reads
IsoQuant is a tool for the genome-based analysis of long RNA reads, such as PacBio or Oxford Nanopores. IsoQuant allows reconstructing and quantifying transcript models with high precision and decent recall. If the reference annotation is given, IsoQuant also assigns reads to the annotated isoforms based on their intron and exon structure. IsoQuant further performs annotated gene, isoform, exon, and intron quantification. -
2
Weinberg-R2R
Faster creation of aesthetic RNA secondary structure diagrams
R2R is a program to assist in aesthetic drawings of RNA secondary structures. It is primarily aimed at drawing consensus diagrams, but can also draw single RNA molecules. R2R is freely available under the GNU Public License, and runs as a command-line program under UNIX-like systems such as Linux, MacOS Darwin or Cygwin on Windows. R2R was written by Zasha Weinberg. If you use it, please cite this paper: http://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-12-3 -
3
sRNAWorkbench
The UEA sRNA Workbench
A suite of tools for analysing small RNA (sRNA) data from Next Generation Sequencing devices. Including expression profiling of known mirco RNA (miRNA), identification of novel miRNA in deep-sequencing data and identification of other interesting landmarks within high-throughput genetic data -
4
TI2BioP allows mainly the calculation of topological indices (spectral moments) derived from inferred and artificial 2D structures of DNA, RNA and proteins being possible to carry out a structure-function correlation irrespective of sequence alignments. TI2BioP version 3.0 is a python platform with a graphical interface designed for Windows, Linux and Mac OS.
-
MongoDB Atlas runs apps anywhereMongoDB Atlas gives you the freedom to build and run modern applications anywhere—across AWS, Azure, and Google Cloud. With global availability in over 115 regions, Atlas lets you deploy close to your users, meet compliance needs, and scale with confidence across any geography.
-
5
Weinberg-CMfinder
Predict and score RNA secondary structures
The CMfinder package is a suite of programs with two main purposes: (1) the cmfinder program infers an alignment and consensus secondary structure of an RNA, using unaligned sequences as input. (2) other tools score alignments to indicate evidence of RNA secondary structure within the alignment. RNAphylo assigns a probabilistic score to an existing alignment, using an explicit phylogenetic model. hmmpair assigns a score based on evidence of covariation that is supported by sequence conservation. ... -
6
packeis
Check for selection of RNA secondary structure
PACKEIS is a software that allows us to assess whether or not a coding sequence represents an extreme solution in terms of backfolding, considering the alternative coding sequences that could have been realized by evolution in order to encode the given peptide sequence based on usage of synonymous codons. -
7
BNNPT
A powerful method for nonlinear dependence of two continuous variables
...We addressed this research question by using BNNPT (Bagging Nearest-Neighbor Prediction Test, software available at https://sourceforge.net/projects/bnnpt/). In the BNNPT framework, we first used the value of X to construct a bagging neighborhood structure. And then, we got the out of bag estimator of Y based on the bagging neighborhood structure. The square error was calculated to measure how good Y is predicted by X. Finally, permutation test was applied to detect the significance of the observed square error. To evaluate the strength of BNNPT compared to seven other methods, we performed extensive simulations to explore the relationship between methods and compared the false positive rates and statistical power using both simulated and real RNA-seq datasets. -
8
RNAfdl
RNA force directed layout
RNAfdl is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. RNAfdl allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. In addition, RNAfdl allows you to incorporate non-canonical base pairs into drawings. -
9
faif
C++ header only library with AI and bioinformatics algorithms
C++ header only library, small and fast; Naive Bayesian Classifier, Decision Tree Classifier (ID3), DNA/RNA nucleotide second structure predictor, timeseries management, timeseries prediction, generic Evolutionary Algorithm, generic Hill Climbing algorithm and others. -
Catch Bugs Before Your Customers DoMove from alert to fix before users notice. AppSignal monitors errors, performance bottlenecks, host health, and uptime—all from one dashboard. Instant notifications on deployments, anomaly triggers for memory spikes or error surges, and seamless log management. Works out of the box with Rails, Django, Express, Phoenix, Next.js, and dozens more. Starts at $23/month with no hidden fees.
-
10
MaxInfo
Transcriptome assembler for RNA-seq
MaxInfo is an automated transcript discovery and quantification software designing for high-throughput RNA sequencing (RNA-seq). Assembling transcripts from reads are challenging because of the unpredictable uncertainties arising from completing full genome structure with very partial observations. MaxInfo tackles this problem by explicitly reducing the inherent uncertainties in the biological system caused by missing information. -
11
-
12
...It uses as input the coverage files generated by the software ORA (https://sourceforge.net/projects/transcriptomeassemblyora/files/) (Sardu A, Treu L, Campanaro S. Transcriptome structure variability in Saccharomyces cerevisiae strains determined with a newly developed assembly software. BMC Genomics. 2014; 15:1045.)
-
13
RNAstructure
Predict and analyze RNA secondary structures.
This is a software package for the analysis and prediction of RNA secondary structure. -
14
FRETtranslator
Translate smFRET trajectories into RNA secondary strucutures
FRETtranslator is a frame work that allows you to predict a sequence of RNA seondary structure transitions for a given smFRET trajectory. At its core it uses Viterbi-decoding. FRETtranslator combines smFRET data with RNA secondary structure predictions and RNA 3D structure sampling. As such it relies on input from additional software for RNA secondary structure and 3D structure predictions. -
15
A Scalable Multicore Code for RNA Secondary Structure Prediction
-
16
RnaViz is a user-friendly, portable, GUI program for producing publication-quality secondary structure drawings of RNA molecules. Drawings can be created starting from DCSE alignment files if they incorporate structure information or from mfold ct files.
-
17
ViNSS View
Vienna Notation Secondary Structure Viewer
ViNSS View is a highly flexible tool for drawing RNA secondary structures. Secondary structures can be visualized as classical secondary structure plot, circle plot, linear plot or mountain plot. ViNSS View allows manual editing and several drawing styles, as well as a fully automated conjugate gradients minimization approach to draw more complex structures without user interaction. -
18
BoulderALE is an RNA alignment editor, which allows for the annotation of basepairs, annotation and collapsing of features (horizontal) and sequences (vertical), along with 2D display of sequences and base composition given a secondary structure.
-
19
The sibRNAfold program is a modification of the Vienna RNAfold program for RNA secondary structure prediction through energy minimization.
-
20
YaSeTo implements a modification of the widely used Sankoff-Algorithm for sequence/structure alignments of RNA sequences. It is suitable for genome-wide ncRNA gene finding, in case the ncRNA exhibits a conserved secondary structure.
-
21
FRASS is developed for RNA Structure Comparison. It allows one to compare the 3D structures of two RNA molecules and to scan a database containing all the known RNA 3D structures against a single query.
-
22
BARNACLE is a Python library for RNA 3D structure prediction. It can be used for probabilistic sampling of RNA structures that are compatible with a given nucleotide sequence and that are RNA like on a local length scale.
-
23
DNAlyzer is a program that contains two main functions - completing the missed DNA pairs and decode the RNA structure to codones. Each result can be saved as image. DNAlyzer written in VB.NET using .NET Framework 2.0.
-
24
RAINIER: Rapid Automated Inference of Nucleic-Acid Interaction Energy using Refinement RAINIER is a protein simulator that can predict the interface structure of DNA- and RNA-binding proteins, using statistical and physical techniques.
-
25
