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Proprietary, freeware for education, research, nonprofit ALE manual alignment ; some software assistance: Nucleotides: Local: J. Blandy and K. Fogel: 1994 (latest version 2007) Free, GPL2 ALLALIGN For DNA, RNA and protein molecules up to 32MB, aligns all sequences of size K or greater, MSA or within a single molecule.
The Allosteric RNA Designer (ARDesigner) is a web-based tool that solves the inverse folding problem by incorporating mutational robustness. Beside a local search the software has been equipped with a simulated annealing approach to effectively search for good solutions. The tool has been used to design RNA thermometer. [dead link ] [214]
rDiff is a tool that can detect differential RNA processing (e.g. alternative splicing, polyadenylation or ribosome occupancy). RNASeqPower Calculating samples Size estimates for RNA Seq studies. R package version. RNA-Skim RNA-Skim: a rapid method for RNA-Seq quantification at transcript-level. rSeq rSeq is a set of tools for RNA-Seq data ...
In bioinformatics, BLAST (basic local alignment search tool) [3] is an algorithm and program for comparing primary biological sequence information, such as the amino-acid sequences of proteins or the nucleotides of DNA and/or RNA sequences.
First, convert each template DNA base to its RNA complement (note that the complement of A is now U), as shown below. Note that the template strand of the DNA is the one the RNA is polymerized against; the other DNA strand would be the same as the RNA, but with thymine instead of uracil. DNA -> RNA A -> U T -> A C -> G G -> C A=T-> A=U Then ...
RNA Isolation: RNA is isolated from tissue and mixed with Deoxyribonuclease (DNase). DNase reduces the amount of genomic DNA. The amount of RNA degradation is checked with gel and capillary electrophoresis and is used to assign an RNA integrity number to the sample. This RNA quality and the total amount of starting RNA are taken into ...
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 ...
Transcription is the process of copying a segment of DNA into RNA for the purpose of gene expression. Some segments of DNA are transcribed into RNA molecules that can encode proteins, called messenger RNA (mRNA). Other segments of DNA are transcribed into RNA molecules called non-coding RNAs (ncRNAs).