PromoterPlot -- a graphical display of promoter similarities by pattern recognition
What you can do:
Visualize sequence similarities among a group of promoters.
Highlights:
- PromoterPlot is a web-based tool for simplifying the display and processing of transcription factor searches using either the commercial or free TransFac distributions.
- The input sequence is a TransFac search (public version) or FASTA/Affymetrix IDs (local install).
- It uses an intuitive pattern recognition algorithm for finding similarities between groups of promoters by dividing transcription factor predictions into conserved triplet models.
- To minimize the number of false-positive models, it can optionally exclude factors that are known to be unexpressed or inactive in the cells being studied based on microarray or proteomic expression data.
- The program will also estimate the likelihood of finding a pattern by chance based on the frequency observed in a control set of mammalian promoters we obtained from Genomatix.
- The results are stored as an interactive SVG web page on our server.
Keywords:
- transcription factor binding sites transcription factor binding site analysis tool
- DNA-binding sites
- cis-elements
- cis-regulatory elements
- promoter visualization tool
- promoter elements visualization tool
- transcription factors
- response elements
- cis-elements
- cis-regulatory modules analysis tool
- eukaryotic promoters
- mammalian promoters
Literature & Tutorials:
This record last updated: 11-21-2005