(see also: DNA MOTIFS )
Transcription factor binding sites: several sites are available but I have not been particular impressed with the results when analyzing prokaryotic sequences
Tfsitescan (Institute for Transcriptional Informatics, Pittsburgh, U.S.A.) - This tool is intended for promoter sequence analysis and works best with sequences of ~500 nt.
PLACE (National Institute of Agrobiological Sciences, Japan) - Plant cis-acting regulatory DNA elements. PlnTFDB - Plant Transcriptional Factor Database - allows BLAST searching (Reference: P. Pérez-Rodríguez et al. 2009 Nucl. Acids Res. 38: D822-D872) or here for related site.
DBD: Transcription factor prediction database (Gesellschaft für Biotechnologische Forschung mbH (GBF), Braunschweig, Germany) (Reference: D. Wilson et al. 2010. Nucl. Acids Res. 36: D88-D92)
rVista (Comparative Genomics Center, Lawrence Livermore National Laboratory, U.S.A.) - High-throughput discovery of functional regulatory elements in sequence alignments. Excluding up to 95% false positive transcription factor binding sites predictions while maintaining high sensitivity of the search.
CONREAL - allows identification of transcription factor binding sites (TFBS) that are conserved between two [orthologous promoter] sequences. The predictions can be performed by four different methods (CONREAL-, LAGAN-, MAVID- and BLASTZ-based) and results can be compared to each other. (Reference: Berezikov E, et al. 2005. Nucl. Acids Res. 33(Web Server issue):W447-50.)
TFmiR - for deep and integrative analysis of combinatorial regulatory interactions between transcription factors, microRNAs and target genes that are involved in disease pathogenesis. (Reference: Hamed, M. et al. 2015. Nucl. Acids Res.).
TRANSFAC -offers academic and non-profit organizations free access to TRANSFAC® non-professional 2005 version with much reduced functionality and content compared to our professional database. Provides access to programs including Match which is a weight matrix-based program for predicting transcription factor binding sites (TFBS) in DNA sequences. It uses a library of positional weight matrices from TRANSFAC® Public 6.0; and, P-Match - a program for predicting transcription factor binding sites (TFBS) in DNA sequences that combines pattern matching and weight matrix approaches. It uses a library of positional weight matrices from TRANSFAC® Public 6.0 along with the site alignments associated with these matrices.
DOOR2 - Database of prOkaryotic OpeRons - offers high-performance web service for online operon prediction on user-provided genomic sequences; and, an intuitive genome browser to support visualization of user-selected data. Plus a huge database of transcriptional units. (Reference: X. Mao et al. 2014. Nucleic Acids Res. 42(Database issue): D654-9).