The MEME Suite
نویسندگان
چکیده
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.
منابع مشابه
MEME Suite: tools for motif discovery and searching
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. Three sequence scanning algorithms--MAST, FIMO and GLAM2SCAN--allow scannin...
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MOTIVATION Advances in high-throughput sequencing have resulted in rapid growth in large, high-quality datasets including those arising from transcription factor (TF) ChIP-seq experiments. 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. RESULTS The MEME-ChIP web service is designed t...
متن کاملExercise: Behavior and Limitations of Motif Finding
Today, we’ll look at some behaviors of the popular MEME motif-finding software. MEME is a powerful tool for discovering putative regulatory motifs in DNA sequences. You can find it at http://meme-suite.org/tools/meme. To begin, we’ll focus on a motif-finding problem in D. melanogaster promoter sequences. The sequences we will work with are in the FASTA-formatted file dmel-promoters.fna. These s...
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Motivation: The repetitive nature of plant disease resistance genes encoding for nucleotidebinding leucine-rich repeat (NLR) proteins hampers their prediction with standard gene annotation software. Motif alignment and search tool (MAST) has previously been reported as a tool to support annotation of NLR-encoding genes. However, the decision if a motif combination represents an NLR protein was ...
متن کاملDREME: motif discovery in transcription factor ChIP-seq data
MOTIVATION Transcription factor (TF) ChIP-seq datasets have particular characteristics that provide unique challenges and opportunities for motif discovery. Most existing motif discovery algorithms do not scale well to such large datasets, or fail to report many motifs associated with cofactors of the ChIP-ed TF. RESULTS We present DREME, a motif discovery algorithm specifically designed to f...
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