The MEME Suite
TLDR
The capabilities of all the tools within the MEME suite are described, advice on their best use is given and several case studies are provided to illustrate how to combine the results of various MEME Suite tools for successful motif-based analyses.Abstract:
The MEME Suite is a powerful, integrated set of web-based tools for studying sequence motifs in proteins, DNA and RNA. Such motifs encode many biological functions, and their detection and characterization is important in the study of molecular interactions in the cell, including the regulation of gene expression. Since the previous description of the MEME Suite in the 2009 Nucleic Acids Research Web Server Issue, we have added six new tools. Here we describe the capabilities of all the tools within the suite, give advice on their best use and provide several case studies to illustrate how to combine the results of various MEME Suite tools for successful motif-based analyses. The MEME Suite is freely available for academic use at http://meme-suite.org, and source code is also available for download and local installation.read more
Citations
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Interactive Tree Of Life (iTOL) v5: an online tool for phylogenetic tree display and annotation.
TL;DR: The Interactive Tree Of Life (ITOL) as mentioned in this paper is an online tool for the display, manipulation and annotation of phylogenetic and other trees, which allows users to draw shapes, labels and other features directly onto the trees.
Journal ArticleDOI
JASPAR 2020: update of the open-access database of transcription factor binding profiles
Oriol Fornes,Jaime A. Castro-Mondragon,Aziz Khan,Robin van der Lee,Xi Zhang,Phillip A. Richmond,Bhavi P. Modi,Solenne Correard,Marius Gheorghe,Damir Baranasic,Walter Santana-Garcia,Ge Tan,Jeanne Chèneby,Benoit Ballester,François Parcy,Albin Sandelin,Boris Lenhard,Boris Lenhard,Wyeth W. Wasserman,Anthony Mathelier,Anthony Mathelier +20 more
TL;DR: In this 8th release of JASPAR, the CORE collection has been expanded with 245 new PFMs, and 156 PFMs were updated, and the genomic tracks, inference tool, and TF-binding profile similarity clusters were updated.
Journal ArticleDOI
HOCOMOCO: towards a complete collection of transcription factor binding models for human and mouse via large-scale ChIP-Seq analysis
Ivan V. Kulakovskiy,Ivan V. Kulakovskiy,Ivan V. Kulakovskiy,Ilya E. Vorontsov,Ivan S. Yevshin,Ruslan N. Sharipov,Ruslan N. Sharipov,Alla D. Fedorova,Eugene I. Rumynskiy,Eugene I. Rumynskiy,Yulia A. Medvedeva,Yulia A. Medvedeva,Arturo Magana-Mora,Arturo Magana-Mora,Vladimir B. Bajic,Dmitry Papatsenko,Fedor A. Kolpakov,Vsevolod J. Makeev,Vsevolod J. Makeev,Vsevolod J. Makeev +19 more
TL;DR: A nearly doubled volume of published in vivo experiments on transcription factor (TF) binding is profited from to expand the repertoire of binding models, replace low-quality models previously based on in vitro data only and cover more than a hundred TFs with previously unknown binding specificities.
Journal ArticleDOI
AnimalTFDB 3.0: a comprehensive resource for annotation and prediction of animal transcription factors.
TL;DR: The new version of AnimalTFDB provides a comprehensive annotation and classification of TFs and cofactors, and will be a useful resource for studies of TF and transcription regulation.
Journal ArticleDOI
JASPAR 2022: the 9th release of the open-access database of transcription factor binding profiles.
Jaime A. Castro-Mondragon,Rafael Riudavets-Puig,Ieva Rauluseviciute,Roza Berhanu Lemma,Laura Turchi,Romain Blanc-Mathieu,Jérémy Lucas,Paul Boddie,Aziz Khan,Nicolás Manosalva Pérez,Oriol Fornes,Tiffany Y. Leung,Alejandro Aguirre,Fayrouz Hammal,Daniel Schmelter,Damir Baranasic,Benoit Ballester,Albin Sandelin,Boris Lenhard,Klaas Vandepoele,Wyeth W. Wasserman,François Parcy,Anthony Mathelier,Anthony Mathelier +23 more
TL;DR: JASPAR (http://jaspar.genereg.net/) is an open-access database containing manually curated, non-redundant transcription factor (TF) binding profiles for TFs across six taxonomic groups as mentioned in this paper.
References
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Journal ArticleDOI
MEME Suite: tools for motif discovery and searching
Timothy L. Bailey,Mikael Bodén,Fabian A. Buske,Martin C. Frith,Charles E. Grant,Luca Clementi,Jingyuan Ren,Wilfred W. Li,William Stafford Noble +8 more
TL;DR: The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps, and all of the motif-based tools are now implemented as web services via Opal.
Proceedings Article
Fitting a mixture model by expectation maximization to discover motifs in biopolymers.
Timothy L. Bailey,Charles Elkan +1 more
TL;DR: The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.
Journal ArticleDOI
Genomic expression programs in the response of yeast cells to environmental changes.
Audrey P. Gasch,Paul T. Spellman,Camilla M. Kao,Orna Carmel-Harel,Michael B. Eisen,Gisela Storz,David Botstein,Patrick O. Brown +7 more
TL;DR: Analysis of genomic expression patterns in the yeast Saccharomyces cerevisiae implicated the transcription factors Yap1p, as well as Msn2p and Msn4p, in mediating specific features of the transcriptional response, while the identification of novel sequence elements provided clues to novel regulators.
Journal ArticleDOI
FIMO: scanning for occurrences of a given motif.
TL;DR: Find Individual Motif Occurrences (FIMO), a software tool for scanning DNA or protein sequences with motifs described as position-specific scoring matrices, and provides output in a variety of formats, including HTML, XML and several Santa Cruz Genome Browser formats.
Journal ArticleDOI
Genome-Wide Mapping of in Vivo Protein-DNA Interactions
David S. Johnson,Ali Mortazavi,Ali Mortazavi,Richard M. Myers,Richard M. Myers,Barbara J. Wold,Barbara J. Wold +6 more
TL;DR: A large-scale chromatin immunoprecipitation assay based on direct ultrahigh-throughput DNA sequencing was developed, which was then used to map in vivo binding of the neuron-restrictive silencer factor (NRSF; also known as REST) to 1946 locations in the human genome.