[%INCLUDE "sample_t_seqs.html"%] [%INCLUDE "sample_bg_seqs.html"%]

STEP 1: Enter your sequences

[ HELP ]

Paste fasta formatted sequences (retrieve from Galaxy):




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


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



STEP 3: Select transcription factor binding site cluster parameters

[ HELP ]

Select anchoring [%tax_group_list%] TF

[%tf_list = tf_set.get_matrix_list('name')%]

TFBS Clusters Based on JASPAR Profiles

Collections: [%FOREACH col = collections%]   [%col%] [%END%]

Tax groups: [%FOREACH tax = tax_groups%]   [%tax%] [%END%]

Minimum specificity:  bits (min. [%min_ic%] bits)

TF Families:
All TF families
OR select specific TF famlies:
[%tfc_families = tf_cluster_set.get_tf_families()%]
OR upload a file containing one or more TF families




STEP 4: Select TFBS cluster search parameters

[ HELP ]

Maximum inter-binding distance (max. = [%max_inter_binding_dist%])

Matrix match threshold (min. [%min_threshold%]%):
%

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

Sort results by:
Z-score Fisher 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.