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CompleteMOTIFs specifications

Information


Unique identifier OMICS_00478
Name CompleteMOTIFs
Interface Web user interface
Restrictions to use Academic or non-commercial use
Input format FASTA, BED, GFF
Computer skills Basic
Stability No
Maintained No

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Publication for CompleteMOTIFs

CompleteMOTIFs in publications

 (6)
PMCID: 5354758
PMID: 28038451
DOI: 10.18632/oncotarget.14168

[…] the ar protein (arbss) in lncap cells under treatment with r1881. the average peak height, an indication of the amount of dna bound by the ar, is 30 units. the annotation of the chip-seq data by the completemotifs program has identified 8 peaks that are within 500 kb of the transcription start site (tss) of the sema3c gene, five of which are shown in figure in addition to three other peaks […]

PMCID: 4337573
PMID: 25691594
DOI: 10.1128/mBio.02352-14

[…] default parameters and prokaryote or e. coli as the input motif database. the consensus bola binding motif was further confirmed using other motif search software, such as rsat oligo-analysis (), completemotifs (), chipmunk (), and dreme (). additionally, the determined sequence was tested by inverted motif search using rsat dna pattern matching software ()., β-galactosidase activity assays […]

PMCID: 4022013
PMID: 24555784
DOI: 10.1186/1745-6150-9-4

[…] very low levels of enrichment of binding sites for motif enrichment analysis []. meme-chip used mast [] and ama [] algorithms for visualizing motifs as well as for binding strength analysis [,]., completemotifs [] is a de novo motif finding web tool, which was designed for finding over-represented transcription factor binding motifs from chip-seq. completemotifs is a pipeline system, […]

PMCID: 3783169
PMID: 23821662
DOI: 10.1093/nar/gkt586

[…] because there was a large variation of erα-binding sites across different mcf-7 studies, we merged overlapping binding sites in at least two studies to form a consensus erα cistrome using the completemotifs pipeline (). this approach allowed us to combine the results of several studies to provide a global picture of erα-binding sites., from the mcf-7 cell line, we collected three chip-seq […]

PMCID: 3499360
PMID: 23166515
DOI: 10.1371/journal.pgen.1003061

[…] to test for specific sequence motifs we defined hp1a promoter peaks for genes on the 4th chromosome, region 2l:31 and p2l as 50 bp +/− each hp1a peak center and used these sequences as input in the completemotifs platform. an a/t rich motif was found that was significantly enriched in promoters in chromosome 4, 2l:31 and pericentromeric regions compared to the rest of chromosome 2l (). motif […]


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CompleteMOTIFs institution(s)
Children's Hospital Informatics Program at the Harvard-MIT, Division of Health Sciences and Technology, Department of Medicine, Children's Hospital Boston, Boston, MA, USA

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