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TRANSFAC (TRANScription FACtor database) is a manually curated database of eukaryotic transcription factors, their genomic binding sites and DNA binding profiles. The contents of the database can be used to predict potential transcription factor binding sites .
a Wiki-based database for transcription factor-binding data generated by the ENCODE consortium. database: website [8] hmChIP a database and web server for exploring publicly available human and mouse ChIP-seq and ChIP-chip data. database: website [9] HOCOMOCO: a comprehensive collection of human and mouse transcription factor binding sites ...
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.
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 ...
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.
Gene prediction is one of the key steps in genome annotation, following sequence assembly, the filtering of non-coding regions and repeat masking. [3] Gene prediction is closely related to the so-called 'target search problem' investigating how DNA-binding proteins (transcription factors) locate specific binding sites within the genome.
Primer prediction Nucleic profiles: Nucleic acid profile generation and searching Nucleic repeats: Nucleic acid repeat detection Nucleic restriction: Restriction enzyme sites in nucleotide sequences Nucleic RNA folding: RNA folding methods and analysis Nucleic transcription: Transcription factors, promoters and terminator prediction Nucleic ...
In general, the prediction of bacterial genes is significantly simpler and more accurate than the prediction of genes in eukaryotic species that usually have complex intron/exon patterns. Identifying genes in long sequences remains a problem, especially when the number of genes is unknown. Hidden markov models can be part of the solution. [37]