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 trimmed (central 100bp) input sequences.
TOMTOM output:
HTML plain text XML Motifs from JASPAR CORE 2009 that match motifs MEME discovers.
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.
AME output:
HTML plain text Motif Enrichment Analysis of motifs from JASPAR CORE 2009 enriched in the trimmed (central 100bp) input sequences.
CENTRIMO output:
HTML plain text Central Motif Enrichment Analysis of MEME and DREME motifs in input sequences. The HTML results require a modern browser with full canvas support.
SPAMO output:
(Warnings)
HTML XML Motif spacing analysis of 1st MEME motif to all other MEME and DREME motifs.
SPAMO output:
(Warnings)
HTML XML Motif spacing analysis of 1st DREME motif to all other MEME and DREME motifs.

Data

Input Sequences:
sequences 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.

Commands