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Sleuth is a program for analysis of RNA-Seq experiments for which transcript abundances have been quantified with kallisto. SplicingCompass differential splicing detection using RNA-Seq data. sSeq The purpose of this R package is to discover the genes that are differentially expressed between two conditions in RNA-seq experiments.
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
A program for predicting unique local RNA structures in large sequences with unusually stable folding. 1: None: Yes: sourcecode webserver [153] Xrate: a program for analysis of multiple sequence alignments using phylogenetic grammars, that may be viewed as a flexible generalization of the "Evofold" program. any: Yes: Yes: sourcecode [97] Notes
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.
Ideal DNA/RNA - build an ideal DNA or RNA fragment. Find ligands - find and fit a model to any small molecule which may be bound to the macromolecule. Tools for moving existing atoms: Real space refine zone - optimize the fit of the model to the electron density, while preserving stereochemistry. Regularize zone - optimize stereochemistry.
A software engineering expert said there is little documentation the DNA software used in the Caneiro murder case was tested to see that it works. DNA software used in Caneiro murders 'not ready ...
Data analysis usually requires a combination of bioinformatics software tools (see also List of RNA-Seq bioinformatics tools) that vary according to the experimental design and goals. The process can be broken down into four stages: quality control, alignment, quantification, and differential expression. [ 105 ]
SVM based system to find genes using heterogeneous information: RNA-seq, tiling arrays: Eukaryotes [35] MORGAN: Decision tree system to find genes in vertebrate DNA: Eukaryotes [36] BioNIX: Web tool to combine results from different programs: GRAIL, FEX, HEXON, MZEF, GENEMARK, GENEFINDER, FGENE, BLAST, POLYAH, REPEATMASKER, TRNASCAN ...