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motifSearch specifications


Unique identifier OMICS_32168
Name motifSearch
Software type Application/Script
Interface Graphical user interface
Restrictions to use None
Input data A tab-separated file with deep sequencing data.
Operating system Unix/Linux, Mac OS
Programming languages Python
License GNU General Public License version 3.0
Computer skills Medium
Stability Stable
Maintained Yes




No version available


  • person_outline Katherine Luzuriaga
  • person_outline Liisa Selin

Publication for motifSearch

motifSearch citations


Epigenomic characterization of a p53 regulated 3p22.2 tumor suppressor that inhibits STAT3 phosphorylation via protein docking and is frequently methylated in esophageal and other carcinomas

PMCID: 5743460
PMID: 29290793
DOI: 10.7150/thno.20893

[…] A). Potential binding sites for multiple transcription factors, including p53, c-Myb, heat-shock factor (HSF), STATs, E2F and Sp1, were predicted using TFSEARCH ( and MotifSearch ( (Fig. A), indicating that this promoter is subject to the regulation of these transcription factors. Thus, several segments covering this region were cloned and tested fo […]


Quantifying promoter activity during the developmental cycle of Chlamydia trachomatis

Sci Rep
PMCID: 4893696
PMID: 27263495
DOI: 10.1038/srep27244

[…] d P1 regions.We next searched for the putative promoter (s) from the 607 bp intergenic sequences (IGSs) upstream of the ompA of C. trachomatis strain L2/434/Bu in silico using a dynamic program-based MotifSearch tool. A two-block-motif, TTAACA (−35)-n16–19-TATAAT (−10), was used for C. trachomatis σ66 recognition sequences and motif TAAAGTTT (−35)-n10–14-GTTGACAA (−10) was used for σ28 recognition […]


Characterization of Human Chromosomal Material Exchange with Regard to the Chromosome Translocations Using Next Generation Sequencing Data

Genome Biol Evol
PMCID: 4255766
PMID: 25349267
DOI: 10.1093/gbe/evu234

[…] Motif search for common molecular features was conducted through MotifSearch.Com, an online motif search tool built on the state-of-the-art qPMS7 algorithm (). It adapted one of the most well-known motif search model—Planted Motif Search () which can precisely capt […]


A Large Number of Nuclear Genes in the Human Parasite Blastocystis Require mRNA Polyadenylation to Create Functional Termination Codons

Genome Biol Evol
PMCID: 4159000
PMID: 25015079
DOI: 10.1093/gbe/evu146

[…] that may constitute the polyadenylation signal in a 50-bp region upstream and downstream of the mapped polyadenylation sites were searched using the qPMS7 algorithm for de novo motif search (;, last accessed July 15, 2014). Details on the analyses are provided in supplementary methods, Supplementary Material online. […]


Identification and Expression Profiling of Odorant Binding Proteins and Chemosensory Proteins between Two Wingless Morphs and a Winged Morph of the Cotton Aphid Aphis gossypii Glover

PLoS One
PMCID: 3779235
PMID: 24073197
DOI: 10.1371/journal.pone.0073524

[…] (apterous) Morph II and winged adults (alate) Morph III (). A total of 54,547 unigenes were assembled from 1,113,269 clean reads and 9 putative OBP and 9 putative CSP transcripts identified () using Motifsearch [] and BLAST. We name the OBP genes as AgosOBP2-10 and the CSP genes as AgosCSP1-2 and 4-10 following the nomenclature established for A . pisum []. All of these OBP and CSP transcript […]


Predicting whole genome protein interaction networks from primary sequence data in model and non model organisms using ENTS

BMC Genomics
PMCID: 3848842
PMID: 24015873
DOI: 10.1186/1471-2164-14-608

[…] hloroplast (plant only), vacuole (plant and fungus), and the lysosome (animal only) - along with the raw output from each of the MultiLoc2 subprograms - SVMTarget, SVMSA, SVMaac, PhyloLoc, GOLoc, and MotifSearch. […]


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motifSearch institution(s)
Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA; Department of Pathology, University of Massachusetts Medical School, Worcester, MA, USA; School of Interdisciplinary Informatics, University of Nebraska at Omaha, Omaha, NE, USA
motifSearch funding source(s)
Supported by NIH grant AI-49320, AI-046629, AI-109858, AI038996 and Center for Diabetes Research Core (DR32520), NIAID training grant T32-AI-007349-17, the UMass Center for Clinical and Translational Science (UL1-TR001453), and a Nebraska Research Initiative grant.

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