Discovering Novel Sequence Motifs with MEME

@article{Bailey2002DiscoveringNS,
  title={Discovering Novel Sequence Motifs with MEME},
  author={T. Bailey},
  journal={Current Protocols in Bioinformatics},
  year={2002},
  volume={00}
}
  • T. Bailey
  • Published 2002
  • Biology, Medicine
  • Current Protocols in Bioinformatics
This unit illustrates how to use MEME to discover motifs in a group of related nucleotide or peptide sequences. A MEME motif is a sequence pattern that occurs repeatedly in one or more sequences in the input group. MEME can be used to discover novel patterns because it bases its discoveries only on the input sequences, not on any prior knowledge (such as databases of known motifs). The input to MEME is a set of unaligned sequences of the same type (peptide or nucleotide). For each motif it… Expand
57 Citations
Profile-based short linear protein motif discovery
  • 20
  • PDF
Finding Similar Nucleotide Sequences Using Network BLAST Searches
  • I. Ladunga
  • Medicine
  • Current protocols in bioinformatics
  • 2017
  • 11
  • Highly Influenced
Finding Similar Nucleotide Sequences Using Network BLAST Searches
  • I. Ladunga
  • Medicine, Biology
  • Current protocols in bioinformatics
  • 2009
  • 5
Parallelisation of maximal patterns finding algorithm in biological sequences
  • 1
TFBS detection algorithm using distance metrics based on center of mass and polyphase mapping
  • 2
Visualization and Exploration of Conserved Regulatory Modules Using ReXSpecies 2
  • 4
  • PDF
Motif discovery using expectation maximization and Gibbs' sampling.
  • G. Stormo
  • Mathematics, Medicine
  • Methods in molecular biology
  • 2010
  • 13
Identification of 15 candidate structured noncoding RNA motifs in fungi by comparative genomics
  • 6
DNA Motif Databases and Their Uses
  • G. Stormo
  • Biology, Medicine
  • Current protocols in bioinformatics
  • 2015
  • 17
  • Highly Influenced
  • PDF
...
1
2
3
4
5
...

References

SHOWING 1-9 OF 9 REFERENCES
The Value of Prior Knowledge in Discovering Motifs with MEME
  • 700
  • PDF
Meta-MEME: motif-based hidden Markov models of protein families
  • 210
  • PDF
Combining evidence using p-values: application to sequence homology searches
  • 1,082
  • PDF
Searching databases of conserved sequence regions by aligning protein multiple-alignments.
  • 240
  • Highly Influential
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.
  • 799
  • PDF
A simple method for displaying the hydropathic character of a protein.
  • 18,367
  • PDF
TRANSFAC: an integrated system for gene expression regulation
  • 1,239
  • PDF
The Blocks database--a system for protein classification
  • 136
  • Highly Influential
  • PDF