What is Tfbs?
Abstract. Motivation: TFBS is a set of integrated, object-oriented Perl modules for transcription factor binding site detection and analysis. It implements objects representing specificity profile matrices, binding sites and sets thereof, pattern generators, and pattern database interfaces.
What is the relationship between transfac and promo?
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.
Do promoters bind transcription factors?
RNA polymerase and the necessary transcription factors bind to the promoter sequence and initiate transcription. Promoter sequences define the direction of transcription and indicate which DNA strand will be transcribed; this strand is known as the sense strand.
How do you predict transcription factor binding sites?
Prediction of transcription factor binding sites is generally performed by scanning a DNA sequence of interest with a position weight matrix (PWM) for a transcription factor of interest [6, 7] and various pattern-matching tools have been developed for this purpose.
What is a transcription factor motif?
Transcription factors (TFs) are proteins with DNA binding activity that are involved in the regulation of transcription. A TF has binding preferences to a specific set of DNA sequences referred to as a “binding motif.” TFs have different binding affinities for sequences forming their binding motif set.
Do activators bind to enhancers?
Most activators are DNA-binding proteins that bind to enhancers or promoter-proximal elements. The DNA site bound by the activator is referred to as an “activator-binding site”. The activity of activators can be regulated.
What method can be used to identify where a transcription factor is bound to DNA in the genome?
DNA footprinting
DNA footprinting is an in vitro technique used to examine the binding of proteins to specific regions of DNA. This technique cleverly exploits the fact that when a transcription factor is bound to DNA with a certain affinity, the DNA is protected from degradation by nucleases.
How is promo used to predict transcription factor binding sites?
PROMO is a program to predict transcription factor binding sites in DNA sequences. It can analyse one sequence or multiple related sequences. PROMO (prediction of transcription factor binding sites), ESSEM (assembly of ESTs), pattern search tools, align tools, clustering tools
How is promo used to identify TFBS in DNA?
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.
Where can I find the predicted binding sites for genes?
Predicted best binding sites as well as complete fragments are available in FASTA and BED format via the ChIP Experiment Reports, as are lists of genes in a distance range to the fragments as specified by the user.
Can you use TRANSFAC as an encyclopedia of transcriptional regulation?
You can use TRANSFAC ® as encyclopedia of transcriptional regulation, or as a tool to identify potential TFBSs. The latter can be done with the proven tool Match TM, or with any of the respective modules in the geneXplain platform.