Summary: This category includes tools and databases. These tools allow you to search transcriptional factors from a database or to analyze your DNA sequence to predict transcriptional factor binding sites.
Protocols
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Promo (ALGGEN)
PROMO is a virtual laboratory for the identification of putative transcription factor binding sites (TFBS) in DNA sequences from a species or groups of species of interest. TFBS defined in the TRANSFAC database are used to construct specific binding site weight matrices for TFBS prediction. The user can inspect the result of the search through a graphical interface and downloadable text files.
http://alggen.lsi.upc.es/cgi-bin/promo_v3/promo/pr...
Added: Thu Feb 05 2009, Hits: 17890, Reviews: 0 Write review - TFBIND (Laboratory Head, SNP Research Center, RIKEN, Japan)
Software for searching transcription factor binding sites (including TATA boxes, GC boxes, CCAAT boxes, transcription start sites (TSS)). This tool uses weight matrix in transcription factor database TRANSFAC R.3.4 developed by Dr. Wingender et al, and the cut-offs originally estimated by our research.
http://tfbind.hgc.jp/
Added: Thu Feb 05 2009, Hits: 19185, Reviews: 0 Write review Cached - TFSEARCH (Parallel Application TRC Laboratory , RWCP , Japan)
Searching Transcription Factor Binding Sites (ver 1.3). Given a DNA sequence, it returns potential transcriptional factor binding sites on the sequence.
http://www.cbrc.jp/research/db/TFSEARCH.html
Added: Thu Feb 05 2009, Hits: 17608, Reviews: 0 Write review Cached -
CisOrtho
(Adam Wenick et al. WormBase)
Transcription Factor Binding Site Prediction using Position Weight Matrices and C. elegans/C. briggsae Ortholog-based Filtering (Phylogenetic Footprinting)
http://dev.wormbase.org/db/cisortho/query
Added: Thu Feb 05 2009, Hits: 2075, Reviews: 0 Write review Cached -
Dragon ERE Finder
(Dragon Genome Explorer)
An online program for identification and interactive analyses of estrogen response elements (ERE) in DNA sequences
http://sdmc.lit.org.sg/ERE-V2/index
Added: Thu Feb 05 2009, Hits: 3265, Reviews: 0 Write review -
Match - Public Version
(BIOBASE GmbH)
MatchTM is designed for searching potential binding sites for transcription factors (TF binding sites) nucleotide sequences. Note: This link leads to the login page. Free registration is required for access.
http://www.gene-regulation.com/cgi-bin/pub/program...
Added: Thu Feb 05 2009, Hits: 7376, Reviews: 0 Write review -
MatInspector
(Genomatix)
Search transcription factor binding sites. It requires registration and provides limited number of analysis per month for academic users.
http://www.genomatix.de/products/MatInspector/inde...
Added: Thu Feb 05 2009, Hits: 1120, Reviews: 0 Write review Cached