Tomtom protocols

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Tomtom specifications

Information


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

Documentation


Maintainer


  • person_outline FIMO Team <>

Publications for Tomtom

Tomtom in pipelines

 (22)
2018
PMCID: 5822839
PMID: 29479499
DOI: 10.7717/peerj.4391

[…] were retained (). the tfs identified play an important role in the development of the nervous system including neuronal differentiation, migration and fate specification ()., we also used meme (), tomtom () and gomo (), three motif-based sequence analysis tools from the meme suite of programs to analyse the upstream regulatory region in human, mouse and fugu. meme () identifies motifs based […]

2018
PMCID: 5822839
PMID: 29479499
DOI: 10.7717/peerj.4391

[…] aligned regions. tf binding site matches were identified (in both aligned and non-aligned upstream region of the three species) by matinspector using matrix family library version 11.0., meme (), tomtom () and gomo (), three motif-based sequence analysis tools from the meme suite of programs, were used to analyze the upstream regulatory region in human, mouse and fugu. meme () was used […]

2018
PMCID: 5889037
PMID: 29365169
DOI: 10.1093/molbev/msy010

[…] aligned using the paired-end mapping parameters described above., raw reads were quality filtered and subjected to adapter trimming as described above with mapping performed as described earlier., tomtom v4.12.0 () with default parameters was used to determine similarity of yeast cdei-derived motifs to a library of consensus sites for 203 yeast transcription factors () and to a reb1 motif […]

2017
PMCID: 5429541
PMID: 28507606
DOI: 10.1186/s13072-017-0133-5

[…] enrichment analysis was performed using dreme [] and meme [] within the meme suite v4.11.1 with default parameters specifying list of control sequences. enriched motifs were directly submitted to tomtom [] within the meme suite using default parameters. regression modelling the relationship between cgi methylation in 60–65 µm oocytes and the variables listed in table  was performed in r […]

2017
PMCID: 5659388
PMID: 28481342
DOI: 10.1038/ng.3861

[…] the filter to a value that is more than half of its maximum value. we identified the likely binding protein for the motifs by querying the cis-bp database (accessed on june 12, 2015) using the tomtom v4.10.1 search tool and requiring an fdr q-value < 0.1., the authors wish to thank the members of the tuveson lab, c. vakoc and a. siepel for helpful discussions. dat is a distinguished […]


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Tomtom in publications

 (327)
PMCID: 5954277
PMID: 29764390
DOI: 10.1186/s12864-018-4469-4

[…] conditions can be retrieved from our online database (http://wcchang.itps.ncku.edu.tw/cstfanalysis/). the motif-motif similarity between cstfs and plant cistrome database were estimated by using the tomtom program [, ]., the microarray expressions data including 276 samples for six hormones treatments were downloaded from ricexpro []. a list of rice tf-coding genes were retrieved from planttfdb […]

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

[…] 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 []., additional file 1: additional file 2: additional file 3: additional file […]

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

[…] or “fitness tracker” [title/abstract]) or “quantified movement” [title/abstract]) or “movement counter” [title/abstract]) or “jawbone” [title/abstract]) or “vivoactive” [title/abstract]) or “tomtom” [title/abstract]) or “xiaomi mi band” [title/abstract]) or “accelerometer-based tracker” [title/abstract]) or “moov now” [title/abstract]) or “misfit ray” [title/abstract]) or “nokia go” […]

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

[…] to the log2 scale; this transformation minimizes differences between samples for genes with small counts and normalizes the counts with respect to library size., 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 […]

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 (jaspar_core_2016_plants.meme) (), with an e-value of <0.01. five additional tf binding motifs used in a previous report on a. […]


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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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