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PromoterSweep: a tool for identification of transcription factor binding sites

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Abstract

There are many tools available for the prediction of potential promoter regions and the transcription factor binding sites (TFBS) harboured by them. Unfortunately, these tools cannot really avoid the prediction of vast amounts of false positives, the greatest problem in promoter analysis. The combination of different methods and algorithms has shown an improvement in prediction accuracy for similar biological problems such as gene prediction. The web-tool presented here uses this approach to perform an exhaustive integrative analysis, identification and annotation of potential promoter regions. The combination of methods employed includes searches in different experimental promoter databases to identify promoter regions and their orthologs, use of TFBS databases and search tools, and a phylogenetic footprinting strategy, combining multiple alignment of genomic sequences together with motif discovery tools that were tested previously in order to get the best method combination. The pipeline is available for academic users at the HUSAR open server http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar/. It integrates all of this information and identifies among the huge number of TFBS predictions those, which are more likely to be potentially functional.

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Abbreviations

TFBS:

Transcription factor binding site

TSS:

Transcriptional start site

ID:

Identifier

TP:

True positive

TN:

True negative

FP:

False positive

FN:

False negative

SN:

Sensitivity

SP:

Specificity

CC:

Correlation coefficient

XML:

Extensible markup language

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Author information

Author notes

  1. Endre Barta

    Present address: Apoptosis and Genomics Research Group of the Hungarian Academy of Sciences, Research Center for Molecular Medicine, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary

Authors and Affiliations

  1. Molecular Biophysics, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, 69120, Heidelberg, Germany

    Coral del Val, Oliver Pelz, Karl-Heinz Glatting, Endre Barta & Agnes Hotz-Wagenblatt

  2. Computer Science and Artificial Intelligence, Informatics Faculty, University of Granada, Daniel Saucedo Aranda, 18071, Granada, Spain

    Coral del Val

  3. Agricultural Biotechnology Center, Szent-Györgyi Albert u. 4, 2100, Gödöllő, Hungary

    Endre Barta

Authors
  1. Coral del Val
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  2. Oliver Pelz
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  3. Karl-Heinz Glatting
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  4. Endre Barta
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  5. Agnes Hotz-Wagenblatt
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Corresponding author

Correspondence to Agnes Hotz-Wagenblatt.

Additional information

Dedicated to Professor Sandor Suhai on the occasion of his 65th birthday and published as part of the Suhai Festschrift Issue.

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del Val, C., Pelz, O., Glatting, KH. et al. PromoterSweep: a tool for identification of transcription factor binding sites. Theor Chem Acc 125, 583–591 (2010). https://doi.org/10.1007/s00214-009-0643-8

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  • DOI: https://doi.org/10.1007/s00214-009-0643-8

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