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Peer-reviewedCC BY-NC 4.0NAR Genomics and Bioinformatics

ModCRElib: a standalone package to model cis -regulatory elements

  • Patrick Gohl1
  • Oriol Fornes2
  • Patricia M Bota1
  • Alberto Meseguer1
  • Jaume Bonet1
  • Ruben Molina-Fernández1
  • Joan Planas-Iglesias3,4
  • Altair C Hernández5
  • Oriol Gallego5
  • Narcis Fernandez-Fuentes1,6
  • Baldomero Oliva1
6 affiliations
  1. 1Department of Medicine and Life Sciences, (Structural Bioinformatics Group-GRIB), Universitat Pompeu Fabra , Barcelona, Catalonia 08003 ,
  2. 2Centre for Molecular Medicine and Therapeutics, BC Children’s Hospital Research Institute, Department of Medical Genetics, University of British Columbia , Vancouver, BC V5Z 4H4 ,
  3. 3Loschmidt Laboratories, Department of Experimental Biology and RECETOX, Faculty of Science, Masaryk University , Brno 625 00 ,
  4. 4International Clinical Research Center, St Anne’s University Hospital Brno , Brno 656 916 ,
  5. 5Biophysics in Cell Biology, Department of Medicine and Life Sciences, Universitat Pompeu Fabra , Barcelona, Catalonia 08005 ,
  6. 6Institute of Biological, Environmental and Rural Science, Aberystwyth University , Aberystwyth SY23 3DA ,
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Abstract

The ModCRElib package provides various tools for the analysis and modelling of transcription factor (TF)-DNA and regulatory complex inter-protein interactions. It takes structural information on these interactions to predict TF-binding motifs, generate binding profiles along DNA sequences that score the binding affinity, predict TF-binding sites, and model the structure of higher order regulatory complexes. It is capable of working with a variety of input data formats and sources. The user may follow the analysis pipeline as outlined in the documentation or the user can make use of any of the multiple functionalities in an isolated manner. The package takes the service offered by the ModCRE server and enables users to apply its tools in an unrestricted and customizable manner. In this paper we provide five example uses of ModCRElib. This includes (i) TF-binding affinity prediction, (ii) TF ensemble pattern of bindings (aggregation of motifs), (iii) characterization of specificity in TF-binding sites along target DNA sequences, (iv) modelling TF bound to predicted binding sites, and (v) the generation of statistical potential derived scoring profiles of TF interacting with DNA.

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Cite

BibTeXRIS
BibTeX
@article{gohl2026modcrelib,
  title = {{ModCRElib: a standalone package to model cis -regulatory elements}},
  author = {Patrick Gohl and Oriol Fornes and Patricia M Bota and Alberto Meseguer and Jaume Bonet and Ruben Molina-Fernández and Joan Planas-Iglesias and Altair C Hernández and Oriol Gallego and Narcis Fernandez-Fuentes and Baldomero Oliva},
  journal = {NAR Genomics and Bioinformatics},
  year = {2026},
  month = oct,
  doi = {10.1093/nargab/lqag122},
  url = {https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag122/8960102},
  note = {CC BY-NC 4.0},
}
RIS
TY  - JOUR
TI  - ModCRElib: a standalone package to model cis -regulatory elements
AU  - Patrick Gohl
AU  - Oriol Fornes
AU  - Patricia M Bota
AU  - Alberto Meseguer
AU  - Jaume Bonet
AU  - Ruben Molina-Fernández
AU  - Joan Planas-Iglesias
AU  - Altair C Hernández
AU  - Oriol Gallego
AU  - Narcis Fernandez-Fuentes
AU  - Baldomero Oliva
PY  - 2026
DA  - 2026/10/21
JO  - NAR Genomics and Bioinformatics
DO  - 10.1093/nargab/lqag122
UR  - https://academic.oup.com/nargab/article/doi/10.1093/nargab/lqag122/8960102
AB  - The ModCRElib package provides various tools for the analysis and modelling of transcription factor (TF)-DNA and regulatory complex inter-protein interactions. It takes structural information on these interactions to predict TF-binding motifs, generate binding profiles along DNA sequences that score the binding affinity, predict TF-binding sites, and model the structure of higher order regulatory complexes. It is capable of working with a variety of input data formats and sources. The user may follow the analysis pipeline as outlined in the documentation or the user can make use of any of the multiple functionalities in an isolated manner. The package takes the service offered by the ModCRE server and enables users to apply its tools in an unrestricted and customizable manner. In this paper we provide five example uses of ModCRElib. This includes (i) TF-binding affinity prediction, (ii) TF ensemble pattern of bindings (aggregation of motifs), (iii) characterization of specificity in TF-binding sites along target DNA sequences, (iv) modelling TF bound to predicted binding sites, and (v) the generation of statistical potential derived scoring profiles of TF interacting with DNA.
SN  - 2631-9268
ER  -