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FMotif specifications


Unique identifier OMICS_13792
Name FMotif
Alternative name Fast Motif
Software type Application/Script
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux
Computer skills Advanced
Stability No
Maintained No


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Publication for Fast Motif

FMotif in publications

PMCID: 5741957
PMID: 29273003
DOI: 10.1186/s12863-017-0584-5

[…] %; cintracellular; dinvolve in translation and ribosome biogenesis; eprotein length range between 147 and 232 amino acids with known two functionally important conserved residues (w and p); fmotif domain; gtransferring the electrons from cytochrome c via its binuclear copper a centre to the bimetallic centre of the catalytic subunit 1; hproton-dependent , key to legend: ainterpro […]

PMCID: 5569996
PMID: 28854641
DOI: 10.1093/gbe/evx127

[…] and databases used in this study are listed in , online., the motif discovery method daphnia-cistarget is comprised of two steps: a computationally intensive motif scoring and ranking step, and a fast motif recovery step (see materials and methods). for the motif scoring step, we first define the search space for potential cis-regulatory sequences. we tested our method by delineating two […]

PMCID: 4620437
PMID: 26497381
DOI: 10.1038/srep15555

[…] of a2msio4, all the atoms form tetrahedral units, i.e. every atom is in the center of a tetrahedron and has a coordination number of 4. taking advantage of this structural feature, we used a fast motif-network scheme based on genetic algorithm (ga) to explore the complex crystal structures of these materials. our results provide a more comprehensive tetrahedral structure database […]

PMCID: 4502539
PMID: 26180553
DOI: 10.1186/s13072-015-0015-7

[…] for motifs than the larger dhs sequences and can significantly improve the quality of de novo motif discovery. due to the large number of nucleotides in the sequences we scan, we use extreme [], a fast motif discovery algorithm designed for large sequence datasets. as a demonstration of the effectiveness of this approach, extreme is able to recover motifs that significantly match known […]

PMCID: 4265420
PMID: 25442502
DOI: 10.1186/1471-2164-15-1047

[…] different tfs in different cell types and developmental stages.figure 1, more specifically, first, we identify all possible motifs in each of extended binding peak datasets (figure  a and b) using a fast motif finder. second, we find overrepresented co-occurring motif pairs regardless of their distance in each of the datasets, and call them co-occurring pairs (cps) (figure  b and c). third, […]

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FMotif institution(s)
School of Computer and Information Technology & Beijing Key Lab of Traffic Data Analysis, Beijing Jiaotong University, Beijing, China; Department of Bioengineering/ Bioinformatics, University of Illinois at Chicago, Chicago, IL, USA; Center for Healthcare Studies, Institute for Public Health and Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Division of Health and Biomedical Informatics, Department of Preventive Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, USA; Shanghai Institute of Medical Genetics, Shanghai Children’s Hospital, Shanghai JiaoTong University, Shanghai, China
FMotif funding source(s)
Supported by the National Nature Science Foundation of China (grant n°60905029, 61105055, 61105056, 81230086, and 31071167), the Beijing Natural Science Foundation (grant n°4112046) and the Fundamental Research Funds for the Central Universities.

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