2024-03-28T11:23:14Zhttp://digital.csic.es/dspace-oai/requestoai:digital.csic.es:10261/1362622017-08-31T04:30:30Zcom_10261_75com_10261_6col_10261_1210
DIGITAL.CSIC
author
Contreras-Moreira, Bruno
author
Sebastián Yagüe, Álvaro
funder
European Commission
funder
PLANT-KBBE
2016-09-02T10:34:24Z
2016-09-02T10:34:24Z
2016-08
Contreras-Moreira B, Sebastián A. FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces. In: Hehl R (ed.), Plant Synthetic Promoters (Methods in Molecular Biology 1482: 259-277), New York, Springer Science+Business Media. DOI: 10.1007/978-1-4939-6396-6_17 (2016)
978-1-4939-6394-2 (Print)
ISBN 978-1-4939-6396-6 (Online)
http://hdl.handle.net/10261/136262
10.1007/978-1-4939-6396-6_17
http://dx.doi.org/10.13039/501100000780
FootprintDB is a database and search engine that compiles regulatory sequences from open access libraries of curated DNA cis-elements and motifs, and their associated transcription factors (TFs). It systematically annotates the binding interfaces of the TFs by exploiting protein-DNA complexes deposited in the Protein Data Bank. Each entry in footprintDB is thus a DNA motif linked to the protein sequence of the TF(s) known to recognize it, and in most cases, the set of predicted interface residues involved in specific recognition. This chapter explains step-by-step how to search for DNA motifs and protein sequences in footprintDB and how to focus the search to a particular organism. Two real-world examples are shown where this software was used to analyze transcriptional regulation in plants. Results are described with the aim of guiding users on their interpretation, and special attention is given to the choices users might face when performing similar analyzes.
eng
openAccess
Bioinformatics
transcription factor
DNA binding
DNA motif
PSSM
protein domain
promoter
cis-element
database
open-access
FootprintDB: Analysis of plant cis-regulatory elements, transcription factors, and binding interfaces
capítulo de libro
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URL
https://digital.csic.es/bitstream/10261/136262/1/Contreras-MoreiraB_MethMolBiol-3_2016.pdf
File
MD5
9755711d7ef7e31f44ecb10aca52b2b7
1122248
application/pdf
Contreras-MoreiraB_MethMolBiol-3_2016.pdf