MEME ChIP

We process your sequences through a series of steps to help you identify motifs in your DNA sequences.

If you use MEME-ChIP in your research, please cite the following paper:
Philip Machanick and Timothy L. Bailey, "MEME-ChIP: motif analysis of large DNA datasets", Bioinformatics, 2712, 1696-1697, 2011.

For more detail, see this Tutorial. You may find it helpful to open it in another window while examining your results.

Results

MEME output:
HTML plain text XML Motifs discovered in 600 (randomly chosen) trimmed (central 100bp) input sequences.
TOMTOM output:
HTML plain text XML Motifs from JASPAR CORE 2009 that match motifs MEME discovers.
MAST output:
HTML plain text XML Predicted locations of all MEME motifs (p < 0.0001) in the input sequences.
AMA output:
plain text XML Estimated binding affinity of each MEME motif to each input sequence.
DREME output:
HTML plain text XML Motifs discovered in the trimmed (central 100bp) input sequences.
TOMTOM output:
HTML plain text XML Motifs from JASPAR CORE 2009 that match motifs DREME discovers.
MAST output:
HTML plain text XML Predicted locations of all DREME motifs (p < 0.0001) in the input sequences.
AMA output:
plain text XML Estimated binding affinity of each DREME motif to each input sequence.
AME output:
HTML plain text Motifs from JASPAR CORE 2009 enriched in the trimmed (central 100bp) input sequences.
CENTRIMO output:
HTML plain text MEME and DREME motif centrality in the input sequences. The HTML results require a modern browser with full canvas support.

Data

Input Sequences:
sample-dna-Klf1.fa Your original untrimmed sequences.
fasta-center output:
seqs-centered Your sequences centered and trimed to width 100.
fasta-dinucleotide-shuffle output:
seqs-shuffled The centered sequences randomly shuffled maintaining their dinucleotide frequency, used as a background for DREME and AME.
AME input:
seqs-centered_w_bg The centered sequences followed by the same sequences after dinucleotide shuffling.
fasta-subsample (used) output:
seqs-sampled A random sample of 600 of the centered sequences, used by MEME.
fasta-subsample (discarded) output:
seqs-discarded The centered sequences omitted from the sample used by MEME.

Commands