peak-motifs pr

peak-motifs  -v 1 -title pr_genes -i $RSAT/public_html/tmp/www-data/2025/03/19/peak-motifs.2025-03-19.101854_2025-03-19.101854_hlFw6q/peak-motifspeak_seq -max_seq_len 1000 -markov auto -disco oligos,positions -nmotifs 5 -minol 6 -maxol 7 -no_merge_lengths -2str -origin center -scan_markov 1 -task purge,seqlen,composition,disco,merge_motifs,split_motifs,motifs_vs_motifs,timelog,archive,synthesis,small_summary,scan -prefix peak-motifs -noov -img_format png -outdir $RSAT/public_html/tmp/www-data/2025/03/19/peak-motifs.2025-03-19.101854_2025-03-19.101854_hlFw6q

Sequence composition (test sequences)

Nb of peaks: 4
Total seq. size: 4 kb
Min length: 1000 bp
Mean length: 1000 bp
Max length: 1000 bp [ seq: converted purged ]
[ lengths: list distrib graph ]

Nucleotide composition profiles

Transition frequencies
Position profiles

[ 1nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

Dinucleotide composition profiles

Transition frequencies
Position profiles

[ 2nt: freq transitions ]
[ bg model: Inclusive format ]
[ profile: table html(individual) ]

motif discovery

oligos_6nt_mkv1

oligos_6nt_mkv1_m1	assembly: cccttc (sig=0.54; e-value=0.29)	RC: gaaggg
oligos_6nt_mkv1_m2	assembly: aaaaga (sig=0.13; e-value=0.74)	RC: tctttt
oligos_6nt_mkv1_m3	: (sig=; e-value=1)	RC:
oligos_6nt_mkv1_m4	: (sig=; e-value=1)	RC:
oligos_6nt_mkv1_m5	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

positions_6nt

Not a single significant pattern

[positions_6nt]

oligos_7nt_mkv1

oligos_7nt_mkv1_m1	assembly: ccgtttc (sig=0.07; e-value=0.85)	RC: gaaacgg
oligos_7nt_mkv1_m2	: (sig=; e-value=1)	RC:
oligos_7nt_mkv1_m3	: (sig=; e-value=1)	RC:
oligos_7nt_mkv1_m4	: (sig=; e-value=1)	RC:
oligos_7nt_mkv1_m5	: (sig=; e-value=1)	RC:

[ discovered words: text ]
[ assembly: text sig matrices ]
[ matrices: tab format transfac format ]

positions_7nt

Not a single significant pattern

[positions_7nt]

Motif discovery

Motif 1 oligos_6nt_mkv1_m1

k-mer sig=0.54; evalue=0.29

bhCCCttCyw

WRGAAGGGDV

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 3 (75.00%)
Max nb of predicted sites per peak: 3
(PR2)
Mean nb of predicted sites per peak: 2.67

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 2 oligos_6nt_mkv1_m2

k-mer sig=0.13; evalue=0.74

gaAAAAGAra

TYTCTTTTTC

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 3 (75.00%)
Max nb of predicted sites per peak: 4
(PR2)
Mean nb of predicted sites per peak: 2.00

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Motif 3 oligos_7nt_mkv1_m1

k-mer sig=0.07; evalue=0.85

maCCGtttCmt

AKGAAACGGTK

[ k-mers: statistics assemblies ]
[ matrix: tab_format transfac_format ]

Predicted sites on test peaks

Distribution of sites

Nb of predicted sites per peak

Nb peaks with at least one predicted site: 3 (75.00%)
Max nb of predicted sites per peak: 2
(PR1)
Mean nb of predicted sites per peak: 1.33

[ sites: text ]
[ distribution: text ]
[ sites per peak: text ]
[ enrichment: text graph ]

Predicted sites on test peaks (all motifs)

[tab]
[bed]

Word significance table
Word comparisons		[tab] [html] [heatmap]
Comparisons between discovered motifs
Discovered motifs versus discovered motifs		[ Discovered motif(s): tf ] [ table: html txt ] [ alignments (logo): html text ] [ clustering: html ] [ graph: gml (for CytoScape) ]

Log files
Parameters and files		[txt] [html]
Time log		[time table] [time log] [html]

Thomas-Chollier M, Herrmann C, Defrance M, Sand O, Thieffry D, van Helden J. (2012). RSAT peak-motifs: motif analysis in full-size ChIP-seq datasets. Nucleic Acids Res 40(4): e31.
Thomas-Chollier M, Darbo E, Herrmann C, Defrance M, Thieffry D, van Helden J. (2012). A complete workflow for the analysis of full-size ChIP-seq (and similar) data sets using peak-motifs. Nat Protoc 7(8): 1551-1568.

RSAT - peak-motifs result

Analysis: pr_genes (19/03/2025 10:19)

Command

Sequence composition

Discovered motifs (by algorithm)

Discovered motifs (with motif comparison)

Motif locations (sites)

Motif comparisons

Logs and parameter files

Publications

Results