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Tomtom specifications


Unique identifier OMICS_08109
Name Tomtom
Interface Web user interface
Restrictions to use None
Input data Query and target motif(s)
Programming languages C
Computer skills Basic
Version 4.11.2
Stability Stable
Maintained Yes



  • person_outline FIMO Team

Publications for Tomtom

Tomtom citations


Delineation of condition specific Cis and Trans acting elements in plant promoters under various Endo and exogenous stimuli

BMC Genomics
PMCID: 5954277
PMID: 29764390
DOI: 10.1186/s12864-018-4469-4

[…] conditions can be retrieved from our online database ( The motif-motif similarity between CsTFs and Plant Cistrome Database were estimated by using the Tomtom program [, ]. […]


Homoeolog expression bias in allopolyploid oleaginous marine diatom Fistulifera solaris

BMC Genomics
PMCID: 5935921
PMID: 29728068
DOI: 10.1186/s12864-018-4691-0

[…] omoters and extracted subgenome independent promoters. To evaluate the biased distribution, Analysis of Motif Enrichment (AME) was used. Functional annotation was performed with Motif Comparison Tool Tomtom against databases of transcription factor binding sites, JASPAR Core 2016 Plants [] and Plant cistrome database []. […]


Physical activity monitors to enhance the daily amount of physical activity in elderly—a protocol for a systematic review and meta analysis

Syst Rev
PMCID: 5932815
PMID: 29720257
DOI: 10.1186/s13643-018-0733-6

[…] itor” OR AB “step monitor” OR AB Pedometer OR AB Fitbit OR AB “activity monitor” OR AB “nokia go” OR AB “misfit ray” OR AB “moov now” OR AB “accelerometer-based tracker” OR AB “xiaomi mi band” OR AB “tomtom” OR AB “vivoactive” OR AB “jawbone” OR AB “movement counter” OR AB “quantified movement” OR AB “fitness tracker” OR AB “activity monitoring device” OR AB (physic* AND activit* AND monitor*) OR […]


Comparative High Resolution Transcriptome Sequencing of Lymphoma Cell Lines and de novo Lymphomas Reveals Cell Line Specific Pathway Dysregulation

Sci Rep
PMCID: 5908872
PMID: 29674676
DOI: 10.1038/s41598-018-23207-7

[…] We used DREME in conjunction with TOMTOM and JASPAR to identify putative transcription factor binding sites (TFBFs) in gene promoters. Gene promoters were defined as 1000-bp-long sequences starting 750 bp upstream and ending 250 bp do […]


Evaluating the Validity of Current Mainstream Wearable Devices in Fitness Tracking Under Various Physical Activities: Comparative Study

PMCID: 5920198
PMID: 29650506
DOI: 10.2196/mhealth.9754

[…] mined the measurement accuracies of six types of wearable devices on 50 subjects walking or running on a treadmill and showed that the wearable devices were very accurate in measuring heart rate; the TomTom Runner Cardio performed the best, with a MAPE of only 0.03, whereas the Fitbit Charge HR performed the poorest, with a MAPE of 0.06. Jo et al [] found that the measurement accuracy of heart rat […]


Plant Lineage Specific Amplification of Transcription Factor Binding Motifs by Miniature Inverted Repeat Transposable Elements (MITEs)

Genome Biol Evol
PMCID: 5950925
PMID: 29659815
DOI: 10.1093/gbe/evy073

[…] The highly enriched words (as well as their complementary words) were transformed to MEME motif format with iupac2meme (from MEME suite; ) and the TF binding motifs identification was performed with TomTom from the MEME suite software with Plant Jaspar Database ( (), with an e-value of <0.01. Five additional TF binding motifs used in a previous report on A. thaliana ( […]


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Tomtom institution(s)
School of Mathematics and Statistics, The University of Sydney, Sydney, NSW, Australia; Institute for Molecular Bioscience, The University of Queensland, Brisbane, QLD, Australia; Department of Genome Sciences, University of Washington, Seattle, WA, USA; Department of Computer Science and Engineering, University of Washington, Seattle, WA, USA
Tomtom funding source(s)
ARC Centre of Excellence in Bioinformatics (to T.L.B.); National Institutes of Health award (R01 RR021692).

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