Overview
(current)
Tools
MyResults
Resources
Tutorials
Public Resources
Downloads
Citations
Team
Login
You must be logged in to begin an analysis.
Visualize TF Sites on Sequences
Email on completion
Predict and visualize TF binding sites on one or multiple enhancers. Sites can be predicted using two approaches. The first and preferred is to predict sites with a core binding site and determine binding site affinity using a reference affinity dataset. When less studies on the TF have been performed, the alternative approach is to use a PWM to predict locations and binding scores. The output is (1) an image visualizing where the predicted sites are along with their affinity or PWM-binding score, and (2) a table with every binding site, its location, direction, affinity and a unique site identifier.
Links:
Tutorial Video
Documentation
Enter Enhancer DNA sequence(s)
DNA sequence(s) to annotate
One or more named DNA sequences to be annotated.
Manually enter table
Upload a file
download example
Sequence name
*
Name of the Enhancer.
Sequence
*
DNA Sequence of the Enhancer. Only A/T/C/G characters allowed (lowercase will be converted to uppercase). Maximum 2000 characters.
0/2000 characters
Maximum 2000 characters allowed
Only A, T, C, G characters allowed. Invalid characters filtered automatically.
Add Row
Annotate TF with relative affinity
Do not use relative affinity
All TFs
Enter your own TFs
Select TFs within tissues
Affinity Normalization
*
Signal-to-noise
Relative
TF Family
*
Select TF family.
TF PBM Dataset
*
Select TF PBM dataset.
Core Site
*
IUPAC formatted core binding site.
Color
*
color options
Color of the predicted TFBS plotted.
Minimum Affinity
Threshold affinity of predicted TFBS to keep.
Select family
Select dataset
Select All
Select core site
Add Row
Add new Normalized tfsite and core to community generated data.
Select all TFs from dataset using the selected normalization.
Processing all TFs, please wait...
Affinity Normalization
Signal-to-noise
Relative
Select Organism
Select Time
Select Organ
Select Cell
Add Selection
Groups
TFs to Analyze
Affinity Normalization
Signal-to-noise
Relative
Annotate TF with PWM binding scores
*
Select PWM annotation method:
Do not use PWMs
All TFs
Selected TFs based on keywords
Subset TFs based on expression data
database to use
Either JASPAR, HOCOMOCO or Dimers.
Choose Database
Jaspar Vertebrates 2026
Jaspar Vertebrates 2024
HOCOMOCO14 Core Motifs
HOCOMOCO13 Core Motifs
Dimers (CAP-SELEX Taipale Lab 2025)
download example
Select Organism
Select Family
Select Type
Select Factor
Add Selection
Selected Motif Categories
Motifs to Include
List of keywords to filter
Keywords to indicate which PWMs to filter for. Keywords can either be TF name, family, or matrix ID.
Select Organism
Select Time
Select Organ
Select Cell
Add Selection
Groups
TFs to Analyze
Affinity Normalization
Signal-to-noise
Relative
Background nucleotide frequencies
What background frequencies of nucleotides. Description of background frequencies here.
Human genome
Mouse genome
Choose your own
A:
T:
G:
C:
Pwm minimum score
Required PWM score to predict a site. Does not apply to PWMs referenecd in the "tf information tsv" file. Default is 0.7.
Pwm binding site color
Color of sites for PWMs. Default is grey.
Other Parameters
Output images as SVG
Option to output images as SVG in addition to PNG. SVG are preferable for manuscript preparation.
True
False
Plot resolution
Enter the resolution for the plot in DPI (dots per inch).
Zoom range
Optional: Given a start position and an end position, zoom into a portion of the sequence. The numbers in the range are inclusive. For example, the first 200 nucleotides of the sequence would be specified as: 1-200. Leave blank if not applicable.
Submit