title: GREAT: a web portal for Genome Regulatory Architecture Tools.
abstract: GREAT (Genome REgulatory Architecture Tools) is a novel web portal for tools designed to generate user-friendly and biologically useful analysis of genome architecture and regulation. The online tools of GREAT are freely accessible and compatible with essentially any operating system which runs a modern browser. GREAT is based on the analysis of genome layout -defined as the respective positioning of co-functional genes- and its relation with chromosome architecture and gene expression. GREAT tools allow users to systematically detect regular patterns along co-functional genomic features in an automatic way consisting of three individual steps and respective interactive visualizations. In addition to the complete analysis of regularities, GREAT tools enable the use of periodicity and position information for improving the prediction of transcription factor binding sites using a multi-view machine learning approach. The outcome of this integrative approach features a multivariate analysis of the interplay between the location of a gene and its regulatory sequence. GREAT results are plotted in web interactive graphs and are available for download either as individual plots, self-contained interactive pages or as machine readable tables for downstream analysis. The GREAT portal can be reached at the following URL https://absynth.issb.genopole.fr/GREAT and each individual GREAT tool is available for downloading.
authors.affiliation: iSSB, CNRS, Genopole, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, Évry 91030 Cedex, France.
authors.forename: Costas
authors.identifier: 0000-0002-7443-3736
authors.initials: C
authors.lastname: Bouyioukos
authors.affiliation: iSSB, CNRS, Genopole, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, Évry 91030 Cedex, France.
authors.forename: François
authors.initials: F
authors.lastname: Bucchini
authors.affiliation: iSSB, CNRS, Genopole, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, Évry 91030 Cedex, France mohamed.elati@issb.genopole.fr.
authors.forename: Mohamed
authors.initials: M
authors.lastname: Elati
authors.affiliation: iSSB, CNRS, Genopole, UEVE, Université Paris-Saclay, 5 rue Henri Desbruères, Évry 91030 Cedex, France francois.kepes@issb.genopole.fr.
authors.forename: François
authors.initials: F
authors.lastname: Képès
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D002874:Chromosome Mapping; D003196:Computer Graphics; D004926:Escherichia coli / Q000235:genetics* / Q000378:metabolism; D016680:Genome, Bacterial; D020407:Internet; D000069550:Machine Learning; D015999:Multivariate Analysis; D011485:Protein Binding; D014157:Transcription Factors / Q000235:genetics* / Q000378:metabolism; D014584:User-Computer Interface
chemical_list: D014157:Transcription Factors