Tomtom pipeline

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

 (5)
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 (gupta et al. 2007) with default parameters was used to determine similarity of yeast cdei-derived motifs to a library of consensus sites for 203 yeast transcription factors (macisaac […]

2016
PMCID: 5175363
PMID: 27655631
DOI: 10.1093/nar/gkw840

[…] the summits of 500-bp sequences from the differential peaks. motif finding was performed using meme-chip (67) with the default parameters. identified motifs were compared with known motifs using tomtom (68) with the default parameters. fimo (find individual motif occurrences) was used to scan for sp1/3/4 and wt1 motif-binding sites (69). mammalian conservation scores for each motif-binding […]

2015
PMCID: 4628360
PMID: 26518232
DOI: 10.1186/s12864-015-2095-y

[…] from differential peaks, excluding dsb-associated peaks. motif finding was performed with meme-chip [49] following default parameters. identified motifs were compared with known motifs using tomtom [93] with a q - value  less than 0.003., all sequencing and gene-chips data from this study are publicly available and have been deposited in the national center for biotechnology information […]

2015
PMCID: 4683654
PMID: 26497144
DOI: 10.1534/g3.115.022517

[…] time point. we then used fimo (grant et al. 2011) to identify the promoter regions of hermaphrodite-enriched genes that contained the acttkaac motif (indicated in table s3). further analysis using tomtom (gupta et al. 2007) to compare the hermaphrodite-enriched motif acttkaac against a database of known motifs identified hlh-2 as a potential trans-acting factor binding this motif. we found […]

2013
PMCID: 3912905
PMID: 23895281
DOI: 10.1111/mmi.12345

[…] 100 bp sequences around the summits of the best peak for each intergenic region for all samples. shuffled input sequences were used for background comparison. significant results were submitted to tomtom (gupta et al., 2007) using default parameters. motif occurrence was confirmed using fimo with a significance threshold of 1e-03 (grant et al., 2011)., rna-seq library preparation […]

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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