Research Tools

• 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://www.wormbase.org/db/cisortho/query
  Added: Wed Mar 21 2007, Hits: 252, 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: Wed Mar 21 2007, Hits: 164, 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: Tue Mar 20 2007, Hits: 325, 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/MatI...
  Added: Tue Mar 20 2007, Hits: 239, Reviews: 0  Write review   Cached
• PMSearch (Poly Matrix Search) (The State Key Laboratory of Pharmaceutical Biotechnology and Model Animal Research Center, Nanjing University)
  A web server for transcription factor binding site prediction. PMSearch utilizes Position Frequency Matrices (PFMs) to predict transcription factor binding sites (TFBSs) in DNA sequences. PMSearch takes PFMs (either user-defined or retrieved from local dataset which currently contains 507 PFMs from Transfac Public 7.0 and JASPAR) and DNA sequences of interest as the input, then scans the DNA sequences with PFMs and reports the sites of high scores as the putative binding sites. The output of the server includes 1) A plot for the distribution of predicted TFBS along the DNA sequence, 2) A table listing location, score and motif for each putative binding site, and 3) Clusters of predicted binding sites. PMSearch also provides links for accessing clusters of PFMs that are similar to the input PFMs to facilitate complicated promoter analysis.
  http://www.nicemice.cn/bioinfo/PMS/
  Added: Wed Mar 21 2007, Hits: 346, Reviews: 0  Write review  
• 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: Tue Mar 20 2007, Hits: 391, 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: Tue Mar 20 2007, Hits: 432, 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: Tue Mar 20 2007, Hits: 440, Reviews: 0  Write review   Cached