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Visualize TF Sites on Sequences
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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
Parameters
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 use upper case A/T/C/G.
Add Row
TF affinity Information
Do not use Affinity information
Manually enter table
Upload info and data files
All the information for the transcription factors being analyzed, including its name, binding site definition, desired color on the plot, any PBM relative affinity data, and any PFM relative score data. You can generate an affinity dataset with the
Normalize TF-DNA Affinity Data
tool.
download example
TF Name
*
Name of the transcription factor.
Color
*
color options
Color of the predicted TFBS plotted.
Core Site
*
IUPAC formatted core binding site (more info[will be hyperlinked])
Affinity Data
create an affinity dataset
Relative or absolute affinity dataset.
download example
Minimum Affinity
Threshold affinity of predicted TFBS to keep.
or
My Affinity datasets
Add Row
tf affinity reference files
File(s) referenced in the TF information file.
download example
Batch Motif Information
Do not use Motif information
Use preloaded Motif databases
Use my Motif database
Upload a Motif database
Batch motif input file
File containing all PFM/PWM matrices to predict binding sites. You can generate a PWM with the
Generate Motif Database
tool.
My Motif databases
Choose Preloaded Database
Jaspar Vertebrates 2024
HOCOMOCO13 Core Motifs
download example
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 image as svg
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.
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