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.
MEME output:
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HTML | plain text | XML | Motifs discovered in trimmed (central 100bp) input sequences. |
TOMTOM output:
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HTML | plain text | XML | Motifs from JASPAR CORE 2009 that match motifs MEME discovers. |
DREME output:
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HTML | plain text | XML | Motifs discovered in the trimmed (central 100bp) input sequences. |
TOMTOM output:
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HTML | plain text | XML | Motifs from JASPAR CORE 2009 that match motifs DREME discovers. |
AME output:
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HTML | plain text | Motif Enrichment Analysis of motifs from JASPAR CORE 2009 enriched in the trimmed (central 100bp) input sequences. | |
CENTRIMO output:
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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. |
Input Sequences:
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sequences | Your original untrimmed sequences. | ||
fasta-center output:
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seqs-centered | Your sequences centered and trimed to width 100. | ||
fasta-dinucleotide-shuffle output:
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seqs-shuffled | The centered sequences randomly shuffled maintaining their dinucleotide frequency, used as a background for DREME and AME. | ||
AME input:
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seqs-centered_w_bg | The centered sequences followed by the same sequences after dinucleotide shuffling. |