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

[ HELP ]

STEP 1: Enter your sequences

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 matrices

[ HELP ]

Select anchoring TF

Select specific JASPAR CORE profile:
[%tf_list = tf_set.get_matrix_list('name')%]
[%tax_group_list%]

OR paste a TFBS profile (retrieve from PAZAR or from JASPAR)

OR upload a file containing a TFBS profile

Select TFs to find in combination with anchoring TF

[%IF num_tax_groups > 1%] All JASPAR CORE profiles from the following tax groups:
[%first_tax_group = 1%] [%FOREACH tax = tax_groups%]   [%tax%] [%first_tax_group = 0%] [%END%]
  with a minimum specificity of  [%ELSE%] All JASPAR CORE [%tax_groups.0%] profiles with a minimum specificity of  [%END%] bits (min. [%min_ic%] bits)

OR select specific profiles:
[%FOREACH tax = tax_groups%] [%IF tax_tf_sets.$tax.size > 0%] [%END%] [%END%] [%FOREACH tax = tax_groups%] [%IF tax_tf_sets.$tax.size > 0%] [%tf_list = tax_tf_sets.$tax.get_matrix_list('name')%] [%END%] [%END%]
[%tax%]

OR paste one or more TFBS profiles (retrieve from PAZAR or from JASPAR)

OR upload a file containing one or more TFBS profiles



STEP 4: Select parameters

[ HELP ]

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

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

Number of results to return:
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.