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Protocols

CollecTF specifications

Information


Unique identifier OMICS_08106
Name CollecTF
Restrictions to use None
Maintained Yes
Wikipedia https://en.wikipedia.org/wiki/CollecTF

Maintainer


  • person_outline CollecTF

Publication for CollecTF

CollecTF citations

 (3)
call_split

Genome Wide Transcriptional Start Site Mapping and sRNA Identification in the Pathogen Leptospira interrogans

2017
PMCID: 5243855
PMID: 28154810
DOI: 10.3389/fcimb.2017.00010
call_split See protocol

[…] that occur zero or one time per sequence, and are found in at leasts two sequences. We then compared motifs against the Swiss Regulon Escherichia coli motifs database (Pachkov et al., ), and against CollecTF, a database of transcription factor binding sites (TFBS) in the Bacteria domain (Kiliç et al., ). The comparison was performed with Tomtom, a motif comparison tool (Gupta et al., ) from the M […]

library_books

G quadruplex prediction in E. coli genome reveals a conserved putative G quadruplex Hairpin Duplex switch

2016
Nucleic Acids Res
PMCID: 5100583
PMID: 27596596
DOI: 10.1093/nar/gkw769

[…] ng sites in the flanking regions in order to find any transcription binding factors associated with the HPGQs. The HPGQ sequences and their flanking regions (±200 bp) were scanned for motifs from the CollecTF (bacterial TF motifs) database using default options (). […]

library_books

The Verrucomicrobia LexA Binding Motif: Insights into the Evolutionary Dynamics of the SOS Response

2016
Front Mol Biosci
PMCID: 4951493
PMID: 27489856
DOI: 10.3389/fmolb.2016.00033

[…] Experimentally validated LexA-binding motifs were downloaded from the CollecTF database (CollecTF, RRID:SCR_014405; Kiliç et al., ). Whole genome shotgun assemblies for Verrucomicrobia species with total sequence lengths larger than or equal to the smallest complete Ver […]

Citations

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CollecTF institution(s)
Department of Biological Sciences, University of Maryland Baltimore County (UMBC), Baltimore, MD, USA

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