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Name Description Knots [Note 1]Links References trRosettaRNA: trRosettaRNA is an algorithm for automated prediction of RNA 3D structure. It builds the RNA structure by Rosetta energy minimization, with deep learning restraints from a transformer network (RNAformer). trRosettaRNA has been validated in blind tests, including CASP15 and RNA-Puzzles, which suggests that the automated predictions ...
Salmon is a software tool for computing transcript abundance from RNA-seq data using either an alignment-free (based directly on the raw reads) or an alignment-based (based on pre-computed alignments) approach. It uses an online stochastic optimization approach to maximize the likelihood of the transcript abundances under the observed data.
Additional functionality include trimming and filtering of raw reads, SNP and InDel detection, mRNA and microRNA quantification and fusion gene detection. Yes Yes Yes Multiprocessor-core, client-server installation possible Proprietary, commercial, free trial version PASS Indexes the genome, then extends seeds using pre-computed alignments of ...
For example, a precursor mRNA (pre-mRNA) is a type of primary transcript that becomes a messenger RNA (mRNA) after processing. Pre-mRNA is synthesized from a DNA template in the cell nucleus by transcription. Pre-mRNA comprises the bulk of heterogeneous nuclear RNA (hnRNA). Once pre-mRNA has been completely processed, it is termed "mature ...
CRISPR-Cas design tools are computer software platforms and bioinformatics tools used to facilitate ... unspliced mRNA, mRNA, 5'UTR, CDS, 3'UTR, unspliced lincRNA ...
RNA-Seq alignment with intron-split short reads. Alignment of short reads to an mRNA sequence and the reference genome. Alignment software has to account for short reads that overlap exon-exon junctions (in red) and thereby skip intronic sections of the pre-mRNA and reference genome.
High performance GPU-accelerated ab initio molecular dynamics and TD/DFT software package for very large molecular or even nanoscale systems. Runs on NVIDIA GPUs and 64-bit Linux, has heavily optimized CUDA code. Proprietary, trial licenses available PetaChem LLC: TINKER: I Yes Yes Yes Yes I I Yes Yes Software tools for molecular design-Tinker ...
ID3-generated decision tree used to determine whether a particular nucleotide pair within a pre-mRNA sequence corresponds to an mRNA splice site. This tree has been shown to have a 95% correct prediction rate. [2] ID3 does not guarantee an optimal solution. It can converge upon local optima.