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Neural network promoter prediction: Prokaryotes, Eukaryotes [38] NNSPLICE: Neural network splice site prediction: Drosophila, Human [39] ORFfinder: Graphical analysis tool to find all open reading frames: Prokaryotes, Eukaryotes [40] Regulatory Sequence Analysis Tools: Series of modular computer programs to detect regulatory signals in non ...
A combination of tools is employed: PALMapper (reads alignment), mTiM and mGene (inference of new transcripts). 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 ...
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 ...
Another application is to retrieve all TFs that regulate a given (set of) gene(s). In the context of systems-biological studies, the TF-target gene relations documented in TRANSFAC were used to construct and analyze transcription regulatory networks. [14] [15] By far the most frequent use of TRANSFAC is the computational prediction of potential ...
Other transcription factors differentially regulate the expression of various genes by binding to enhancer regions of DNA adjacent to regulated genes. These transcription factors are critical to making sure that genes are expressed in the right cell at the right time and in the right amount, depending on the changing requirements of the organism.
Spaced Motif Analysis Tool (SpaMo) is a tool for inferring interactions between transcription factors. SpaMo takes a set of sequences (typically sequences surrounding ChIP-seq peaks), a motif represented in these sequences, and a database of known motifs.
Transcription factor naming issues were addressed through discussion of integration of transcription factor prediction pipelines, such as DBD or flyTF, which have been supplemented with manual curation versus solely manual curated implementations like TFcat.
Nine-amino-acid transactivation domain (9aaTAD) defines a domain common to a large superfamily of eukaryotic transcription factors represented by Gal4, Oaf1, Leu3, Rtg3, Pho4, Gln3, Gcn4 in yeast, and by p53, NFAT, NF-κB and VP16 in mammals. The definition largely overlaps with an "acidic" family definition. A 9aaTAD prediction tool is available.
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