Search Results for "rna" - Page 5
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Showing 135 open source projects for "rna"
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HubSpot is an AI-powered customer platform with all the software, integrations, and resources you need to connect your marketing, sales, and customer service. HubSpot's connected platform enables you to grow your business faster by focusing on what matters most: your customers.
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SKUDONET ADC, operates at the application layer, efficiently distributing network load and application load across multiple servers. This not only enhances the performance of your application but also ensures that your web servers can handle more traffic seamlessly.
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ALEXA-Seq is a method for using massively parallel paired-end transcriptome sequencing for 'alternative expression analysis'.
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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.
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The sibRNAfold program is a modification of the Vienna RNAfold program for RNA secondary structure prediction through energy minimization.
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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.
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DuffyRNAseq is an R package that implements an analysis pipeline for processing RNA-seq data from Illumina NextGen sequencers, to measure gene transcription and differential expression.
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LaJolla can perform 3D alignments of RNA and protein structures. It is fast, simple to use and well tested. LaJolla is successfully published in a peer reviewed journal. !!!!!! PROJECT MOVED TO GITHUB !!!!!! Please check out http://raphaelbauer.github.io/lajolla/
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ICE Cafe is Open sourse sequence cromatgram alginer and viewer. The first purpose of this sofware is to find a RNA Editing by Comparing Genomic sequence to RNA sequence, or by using the ICE method developed at Suzuki Lab,Dept Chem&Biotech Tokyo Univ
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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.
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KrakenD is a high-performance API Gateway optimized for resource efficiency, capable of managing 70,000 requests per second on a single instance. The stateless architecture allows for straightforward, linear scalability, eliminating the need for complex coordination or database maintenance.
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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.
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A colorized interactive dotplot program designed for pair-wise comparisons of RNA & DNA. The original idea was from the mind of late Prof. William J. Dreyer of Caltech. The idea is to be able to see the "tapestry" of life, which comes alive with color.
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This is a reference implementation of snoBAC, a Bayesian Classifier designed to predict box H/ACA snoRNAs in Caenorhabditis nematode genomes. For details of algorithm and data, see Wang and Ruvinsky (2009) RNA in press.
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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.
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TiMAT2 contains tools for low and high level genomic tiling microarray analysis using the Affymetrix, NimbleGen, and Agilent platforms. It is designed for processing single and multi chip data sets from ChIP-Chip, RNA difference, and aCGH experiments.
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Code for predicting the 2-dimensional folding with minimum energy of a given RNA sequence. The code was written and originally released by Rune Lyngso.
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The program predicts the optimal folding of all consecutive substrings of length L of an RNA sequence of length N in O(NL) time. The algorithm is based on two papers: Wexler, Zilberstein, Ziv-Ukelson (2007), and Horesh, Wexler, Ziv-Ukelson ,Unger (2008)
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MIREAP is a tool which can be used to identify both known and novel microRNAs from small RNA libraries deeply sequenced by Solexa/454/Solid technology.
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The software implements a fast optimal co-folding of pairs of RNA sequences. The algorithm is described in details in the paper "A faster algorithm for RNA co-folding" by Ziv-Ukelson, Gat-Viks, Wexler, and Shamir.
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SISSIz is a program for randomizing multiple sequence alignments preserving dinucleotide content. It can be used as a control strategy for comparative noncoding RNA gene prediction programs and as a standalone RNA gene finder.
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The Biomolecule Toolkit is a library for modeling biological macromolecules such as proteins, DNA and RNA. It provides a C++ interface for common tasks in structural biology to facilitate the development of molecular modeling, design and analysis tools.
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ParticleStats is software for analysing tracked particles from RNA Localization experiments. Analysis is performed on the X and Y coordinated of the tracked RNA particles
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mccore is a bioinformatics data structures and tools library for efficient analysis and manipulation of RNA, DNA and protein 3D structures.
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The program siRNArules 1.0 can predict active short interfering RNA (siRNA) with a rather high efficiency (see published paper on this in RNA journal). This project aims to develop new versions, siRNArules 2.0 etc.