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MEME SUITE: tools for motif discovery and searching

T. L. Bailey, M. Boden, F. A. Buske, M. Frith, C. E. Grant, L. Clementi, J. Ren, W. W. Li, W. S. Noble
2009 Nucleic Acids Research  
The MEME Suite web server provides a unified portal for online discovery and analysis of sequence motifs representing features such as DNA binding sites and protein interaction domains.  ...  The popular MEME motif discovery algorithm is now complemented by the GLAM2 algorithm which allows discovery of motifs containing gaps.  ...  ., C.E.G. and W.S.N. acknowledge NIH/NCRR award R01 RR021692 for support of continuing development of the MEME and related sequence analysis tools.  ... 
doi:10.1093/nar/gkp335 pmid:19458158 pmcid:PMC2703892 fatcat:ryullyi7rvhdxircfvrg73e6di

The MEME Suite

Timothy L. Bailey, James Johnson, Charles E. Grant, William S. Noble
2015 Nucleic Acids Research  
The MEME Suite is a powerful, integrated set of webbased tools for studying sequence motifs in proteins, DNA and RNA.  ...  The MEME Suite is freely available for academic use at, and source code is also available for download and local installation.  ...  Comparison with other motif analysis tools Although many motif discovery and search tools have been described in the scientific literature, the MEME Suite is unique in terms of its broad functionality  ... 
doi:10.1093/nar/gkv416 pmid:25953851 pmcid:PMC4489269 fatcat:kgmu2aspjvckvbm6lldm22yb2a

Memes: A motif analysis environment in R using tools from the MEME Suite

Spencer L. Nystrom, Daniel J. McKay, Mihaela Pertea
2021 PLoS Computational Biology  
In addition to interfacing with popular MEME Suite tools, memes leverages existing R/Bioconductor data structures to store the multidimensional data returned by MEME Suite tools for rapid data access and  ...  The MEME Suite is a widely used toolkit for comprehensive analysis of biopolymer motifs; however, these tools are poorly integrated within popular analysis frameworks like the R/Bioconductor project, creating  ...  Acknowledgments We would like to acknowledge Megan Justice, Garrett Graham, and members of the McKay lab for helpful comments and feedback.  ... 
doi:10.1371/journal.pcbi.1008991 pmid:34570758 pmcid:PMC8496816 fatcat:jryrlxfbirfuxhrfco5g4i3je4

MEME-LaB: motif analysis in clusters

Paul Brown, Laura Baxter, Richard Hickman, Jim Beynon, Jonathan D. Moore, Sascha Ott
2013 Bioinformatics  
The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding, and then easily browse and condense the  ...  While there are tools for ab initio discovery of transcription factor binding sites, most do not provide a quick and easy way to study large numbers of clusters.  ...  Several tools exist to perform this task and MEME in particular is a well-recognized suite for motif discovery (Bailey et al., 2006) , but the MEME web-suite offers limited usage on large numbers of clusters  ... 
doi:10.1093/bioinformatics/btt248 pmid:23681125 pmcid:PMC3694638 fatcat:t6tnag2jszcrzifg5w6gorxrvu

MEME: discovering and analyzing DNA and protein sequence motifs

T. L. Bailey, N. Williams, C. Misleh, W. W. Li
2006 Nucleic Acids Research  
MEME (Multiple EM for Motif Elicitation) is one of the most widely used tools for searching for novel "signals" in sets of biological sequences.  ...  Via the same web server, users can also access the Motif Alignment and Search Tool (MAST) to search sequence databases for matches to motifs encoded in several popular formats.  ...  TLB acknowledges support from NIH, R01 RR021692-01 for support of continuing development of MEME and related sequence analysis tools.  ... 
doi:10.1093/nar/gkl198 pmid:16845028 pmcid:PMC1538909 fatcat:lkxmwae3kzbnzdftgilmdsiufm

BioWord: A sequence manipulation suite for Microsoft Word

Laura J Anzaldi, Daniel Muñoz-Fernández, Ivan Erill
2012 BMC Bioinformatics  
Beyond simple sequence manipulation, BioWord integrates functionality ranging from dyad search and consensus logos to motif discovery and pair-wise alignment.  ...  To address this problem, here we have developed BioWord, a macro-enabled self-installing template for Microsoft Word documents that integrates an extensive suite of DNA and protein sequence manipulation  ...  Acknowledgements The authors would like to thank Naim Raja Díaz, for contributing to the development of an early forerunner of BioWord.  ... 
doi:10.1186/1471-2105-13-124 pmid:22676326 pmcid:PMC3546851 fatcat:kl5oghqkv5crfka4htdymqhg6q

MEME-ChIP: motif analysis of large DNA datasets

Philip Machanick, Timothy L. Bailey
2011 Computer applications in the biosciences : CABIOS  
It runs two complementary motif discovery algorithms on the input data-MEME and DREME-and uses the motifs they discover in subsequent visualization, binding affinity and identification steps.  ...  While there are many existing tools for discovering TF binding site motifs in such datasets, most web-based tools cannot directly process such large datasets.  ...  MEME-ChIP complements other web-based ChIP-seq motif analysis tools.  ... 
doi:10.1093/bioinformatics/btr189 pmid:21486936 pmcid:PMC3106185 fatcat:axvds5jydbbwzn22j72kg2p4p4

Identification of Conserved Functional Motifs in Lactoferrin Using Meme

Shashank Rana
2012 International Journal on Bioinformatics & Biosciences  
Our work was on motif discovery by using OOPS modal of MEME (Multiple EM for Motif Elicitation) tool.  ...  It is to be noted that all fifteen sequences contains all three motifs but start points of those are different. Each motif has 15 sites and 50 widths.  ...  The MEME Suite is well known software package with a unified web server interface that enables us to perform all four types of motif analysis wiz 1) motif discovery, 2) motif-motif database searching,  ... 
doi:10.5121/ijbb.2012.2403 fatcat:pwzvn6o7u5gznhzuvpx2zv2cau

Motif-based analysis of large nucleotide data sets using MEME-ChIP

Wenxiu Ma, William S Noble, Timothy L Bailey
2014 Nature Protocols  
MEME-ChIP is a web-based tool for analyzing motifs in large DNA or RNA data sets.  ...  MEME-ChIP performs two complementary types of de novo motif discovery: weight matrix-based discovery for high accuracy; and word-based discovery for high sensitivity.  ...  Acknowledgments This work was supported by the US National Institutes of Health awards R01 RR021692, R01 GM103544 and R01 GM098039.  ... 
doi:10.1038/nprot.2014.083 pmid:24853928 pmcid:PMC4175909 fatcat:5dymd7u64ffppa4zwjeyos5b6a

Helping Students Understand Gene Regulation with Online Tools: A Review of MEME and Melina II, Motif Discovery Tools for Active Learning in Biology

David Treves
2012 Journal of Microbiology & Biology Education  
Students can conduct research on their favorite motif using a variety of motif database search programs such as MAST (Motif Alignment and Search Tool) and TOMTOM (a tool for comparing a DNA motif to a  ...  Melina II (2) is another great motif discovery tool worth a look. Melina II uses the combined power of several motif discovery tools (including MEME) to analyze promoter regions.  ... 
doi:10.1128/jmbe.v13i2.457 pmcid:PMC3577335 fatcat:kg3uun7eebcwhp5atgw3dwfbsu

MARS: Motif Assessment and Ranking Suite for transcription factor binding motifs [article]

Caleb Kipkurui Kibet, Philip Machanick
2016 bioRxiv   pre-print
We describe MARS (Motif Assessment and Ranking Suite), a web-based suite of tools used to evaluate and rank PWM-based motifs.  ...  We have demonstrated the benefit of this web server in motif choice and ranking, as well as in motif discovery. It can be accessed at  ...  Finally, we acknowledge the ENCODE Consortium for making the data available.  ... 
doi:10.1101/065615 fatcat:7balasle3rb67ofmheioyepdk4

The REACT Suite: A Software Toolkit for Microbial REgulon Annotation and Comparative Transcriptomics [chapter]

Peter Ricke, Thorsten Mascher
2012 Functional Genomics  
Acknowledgement The authors would like to thank Tina Wecke for beta-testing of the REACT suite, providing the figures and critical reading of the manuscript.  ...  Development of the REACT suite was enabled by funding from the 'Concept for the future' of the Karlsruhe Institute of Technology (KIT) within the framework of the German Excellence Initiative.  ...  Again, REACT's motif discovery function is just an embedded interface to these freely available and well established tools, which are components of the MEME suite.  ... 
doi:10.5772/48040 fatcat:fzko62axlbe6lfgmqqm4a6anpe

MoMo: Discovery of post-translational modification motifs [article]

Alice Cheng, Charles Grant, Timothy L. Bailey, William Noble
2017 bioRxiv   pre-print
The resulting motifs are presented to the user in an HTML summary with motif logos and linked text files in MEME motif format. Source code and web server available at  ...  Accordingly, many algorithms have been designed to identify these motifs from mass spectrometry data. MoMo is a software tool for identifying motifs among sets of PTMs.  ...  We have developed a software tool, MoMo (for "modification motifs"), to allow MEME Suite users to identify protein PTM motifs. MoMo reimplements two existing modification motif discovery methods.  ... 
doi:10.1101/153882 fatcat:kwilznglvzfazc47dqnmbxhd5i

Improved benchmarks for computational motif discovery

Geir Sandve, Osman Abul, Vegard Walseng, Finn Drabløs
2007 BMC Bioinformatics  
Therefore, robust assessment of motif discovery methods becomes important, both for validation of existing tools and for identification of promising directions for future research.  ...  We show that for many data sets in a recently proposed benchmark suite for motif discovery, none of the common motif models can accurately discriminate the binding sites from remaining sequence.  ...  Acknowledgements We want to thank Kjetil Klepper for help with extracting binding site fragments from TRANSFAC matrix alignments and Jostein Johansen for extensive help with benchmark runs and web site  ... 
doi:10.1186/1471-2105-8-193 pmid:17559676 pmcid:PMC1903367 fatcat:2ylt6fxdungpxjbqr6ex524s3q

Cell-Specific mRNA Profiling of the Caenorhabditis elegans Somatic Gonadal Precursor Cells Identifies Suites of Sex-Biased and Gonad-Enriched Transcripts

Mary B. Kroetz, David Zarkower
2015 G3: Genes, Genomes, Genetics  
Our data illustrate the power of cellspecific transcriptome analysis and suggest that early sex differentiation in the gonad is controlled by a relatively small suite of differentially expressed genes,  ...  The Caenorhabditis elegans somatic gonad differs greatly between the two sexes in its pattern of cell divisions, migration, and differentiation.  ...  FIMO was then used to identify which promoter regions of transcripts contained the DREME-generated motif. All informatics tools can be found at:  ... 
doi:10.1534/g3.115.022517 pmid:26497144 pmcid:PMC4683654 fatcat:3pdh7ekwczaf5bro3kzpxbcxwm
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