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Motif-based sequence analysis tools

Tutorial and training materials by OpenHelix

The MEME suite is a freely available collection of tools that can be used to discover motifs in a set of DNA or protein sequences. MEME stands for Multiple Expectation Maximum for Motif Elicitation. With MEME suite you can: discover motifs in DNA or protein sequences; search sequence databases using a given motifs; compare a given motif to all motifs that are in a motif database; and associate motifs with the Gene Ontology terms that are listed for a motifs putative target genes.
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You'll learn:

  • about the different components of the MEME suite, and how they interconnect
  • how to discover motifs within DNA or protein sequences
  • to align motifs and search for motifs
  • to use the MEME suite to search for motif similarity and GO association


Related tutorials

This tutorial is a part of the tutorial group Motif analysis tools. You might find the other tutorials in the group interesting:

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Recent BioMed Central research articles citing this resource

Fukunaga Tsukasa et al., CapR: revealing structural specificities of RNA-binding protein target recognition using CLIP-seq data. Genome Biology (2014) doi:10.1186/gb-2014-15-1-r16

Yang Peng et al., LDsplit: screening for cis -regulatory motifs stimulating meiotic recombination hotspots by analysis of DNA sequence polymorphisms Sequence analysis (applications). BMC Bioinformatics (2014) doi:10.1186/1471-2105-15-48

Maticzka Daniel et al., GraphProt: modeling binding preferences of RNA-binding proteins. Genome Biology (2014) doi:10.1186/gb-2014-15-1-r17

Inoue Tsuyoshi et al., Cross-enhancement of ANGPTL4 transcription by HIF1 alpha and PPAR beta/delta is the result of the conformational proximity of two response elements. Genome Biology (2014) doi:10.1186/gb-2014-15-4-r63

Fan Chengming et al., Conserved CO-FT regulons contribute to the photoperiod flowering control in soybean Genomics and evolution. BMC Plant Biology (2014) doi:10.1186/1471-2229-14-9

More about the resource:

The MEME suite was originally created by Timothy Bailey from the University of Queensland, Australia and William Stafford Noble from the University of Washington. Currently, the MEME suite continues to be developed and maintained by a group from the University of Queensland, the University of Washington, the University of California at San Diego, the San Diego SuperComputer Center, the NBCR, the CBRC and the National Center for Research Resources.


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The materials and slides offered can not be resold or used for profit purposes. Reproduction, distribution and/or use is strictly limited to instructional purposes only and can not be used for for monetary gain or wide distribution.
Copyright 2009, OpenHelix, LLC.

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