Search Results for "rna" - Page 6

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.

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.

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.

Predicting Global Changes in Transcript Stability Using Time Course Microarray Data

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

mccore is a bioinformatics data structures and tools library for efficient analysis and manipulation of RNA, DNA and protein 3D structures.

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.

free2bind a suite of general purpose bioinformatics tools for computing the minimum free energy (the most stable) binding between two separate RNA molecules.

openSputnik is a robust distributed platform for massive scale precalculation of genetic and genomic data using contemporary bioinformatics methods. Annotated DNA, RNA and protein sequences are stored as binary objects in a variery of relational database

DNA, Amino Acid And RNA Tests: free software for probabilistic measurement and annotation of biological sequences, using phylogenetic Markov chains and stochastic grammars.

Gnome-EMBOSS is an open-source application to help scientists handle DNA, RNA and protein sequences. It uses Gnome/GTK for the user interface and EMBOSS libraries for sequence handling routines. (See www.emboss.org for further info.)

The RNA Ontology Consortium proposed a translation the RNA backbone angles to 46 clusters ('suites') and hence unique names. This project calculates the suites from RNA 3D structures, and to search on a Java-based index structure of known folds.

SeedSearcher: A Discriminative DNA/RNA motif searching tool. SNAP: A Sequence Analysis Platform

A CUDA parallel parser for nondeterministic grammars based on a Bison-generated GLR Parser. Parsing has been used to syntactically analyze programming language. Usually, parsing programming languages is deterministic, i.e., there exists exactly one valid way to syntactically interpret the input. In this project, non-deterministic parsing is used as means to predicting RNA secondary structures. In non-deterministic parsing, more than one syntactic interpretation is valid. This is where...

DawgPack is an ultra-fast, Cloud-based tool that maps many high coverage genomes and performs analysis to find clues for pathogenesis. It will integrate CNV, SNP, RNA-Seq and ChIP-Seq analyses.

A simple tool for molecular biologists (or similar) to estimate the size of electrophoresis gel bands. This can be applied to SDS-Page-,Native-Protein-, DNA, RNA, *whatever* gels as long as a weight/size standard lane is present on the gel.

Danaides stores meta-data from biological banks in a graph databases as well as OBO formatted ontologies. It also provides a web query interface to parse ontologies or extract nodes based on ontology requirements. Example: Get all known elements that are in family of Fish (species ontology) AND a RNA (sequence ontology).