Version 3.0

Sequence-based TFBS Cluster Analysis

Select Analysis Parameters

STEP 1: Enter your sequences

[ HELP ]

Paste fasta formatted sequences (retrieve from Galaxy):




OR upload a file containing a list of fasta formatted sequences:


Optional: Enter the MCP positions for your sequences

[ HELP ]

Paste maximum point of confidence (MCP) positions, in the same order as your sequences.
(1 position/line. To use this option, input sequences must have chromosomal coordinates as IDs. Refer to help for more details.)



OR upload a file containing a list of peak positions (1 position/line):



STEP 2: Enter a background list of sequences

[ HELP ]

Choose a background (sequences randomly selected from experimental control peaks)
OR Paste fasta formatted background sequences (retrieve from Galaxy):




OR upload a file containing a list of fasta formatted background sequences:


Generate a background set of sequences which matches the GC composition of your target sequences using this tool

Optional: Enter the MCP positions for your background sequences

[ HELP ]

Paste maximum point of confidence (MCP) positions, in the same order as your sequences.
(1 position/line. To use this option, input sequences must have chromosomal coordinates as IDs. Refer to help for more details.)



OR upload a file containing a list of peak positions (1 position/line):



STEP 3: Select transcription factor binding site cluster parameters

[ HELP ]

TFBS Clusters Based on JASPAR Profiles

Collections:   CORE   PBM   PENDING

Tax groups:   vertebrates   insects   nematodes

Minimum specificity:  bits (min. 8 bits)

TF Families:

All TF families
OR select specific TF families

OR upload a file containing one or more TF families



STEP 4: Select TFBS cluster search parameters

[ HELP ]

Matrix match threshold (min. 75%):
%

Number of results to display:
Top results
OR only results with Z-score >= and Fisher score >= and KS score >=
(Default values have been chosen based on empirical studies)

Sort results by:
Z-score Fisher score KS score


Please enter your email address:

Press the Submit button to perform the analysis or Reset to reset the analysis parameters to their default values.
The results will be sent to the email address you provided.
Depending on parameters selected and server load, the analysis may take anywhere from a few minutes to several hours to complete.