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TACO specifications

Information


Unique identifier OMICS_22631
Name TACO
Alternative name Transcription factor Association from Complex Overrepresentation
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input format FASTA
Output data A multidimensional view of overrepresented cell-type–specific motif complexes.
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License GNU General Public License version 3.0
Computer skills Advanced
Version 1.0
Stability Stable
Requirements
R math library
Source code URL http://bioputer.mimuw.edu.pl/taco/TACO-1.0.tar.gz
Maintained Yes

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Versioning


No version available

Maintainers


  • person_outline Shyam Prabhakar
  • person_outline Aleksander Jankowski

Additional information


http://bioputer.mimuw.edu.pl/taco/documentation.php https://github.com/ajank/taco

Publication for Transcription factor Association from Complex Overrepresentation

TACO citations

 (3)
library_books

Modular discovery of monomeric and dimeric transcription factor binding motifs for large data sets

2018
Nucleic Acids Res
PMCID: 5934673
PMID: 29385521
DOI: 10.1093/nar/gky027

[…] imary TF and the sites of secondary TFs in ChIP-seq data. The dimer model of iTFs includes relative orientation of the components but it does not consider overlaps and uses binned distances. Finally, TACO’s model includes orientation and distance and allows the components to overlap, but does not analyze the effect of overlap on the binding profile.Using the EM algorithm in motif discovery was ini […]

library_books

Enhanceosome transcription factors preferentially dimerize with high mobility group proteins

2016
BMC Syst Biol
PMCID: 4743414
PMID: 26847699
DOI: 10.1186/s12918-016-0258-3

[…] ined from the ENCODE Project, Genome Browser track wgEncodeUwDnase. The list of DNase I files for human and mouse and the list of corresponding cell types is given in Additional file .Standalone tool TACO [] was provided with all the datasets specified as WeaklySpecificDatasets. As in the default TACO setting, coding regions and repetitive elements were masked, individual DNase peaks were excluded […]

library_books

SOXE transcription factors form selective dimers on non compact DNA motifs through multifaceted interactions between dimerization and high mobility group domains

2015
Sci Rep
PMCID: 4445065
PMID: 26013289
DOI: 10.1038/srep10398

[…] We used our previously developed tool, TACO, to identify overrepresented SOX dimer motifs. We applied our method to a comprehensive collection of DNase-seq datasets from Duke University (Genome Browser track wgEncodeOpenChromDnase) provide […]

Citations

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TACO institution(s)
Computational and Systems Biology, Genome Institute of Singapore, Singapore, Singapore; Faculty of Mathematics, Informatics and Mechanics, University of Warsaw, Warszawa, Poland
TACO funding source(s)
Supported by the Agency for Science, Technology and Research (A*STAR), Singapore; and the National Science Centre, Poland [N N519 652740, 2011/03/N/NZ2/03177, 2012/05/B/ NZ2/00567].

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