[%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:


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 matrices

[ HELP ]

JASPAR CORE Profiles

[%IF num_tax_groups > 1%] All 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 [%tax_group_list%] profiles with a minimum specificity of  [%END%] bits (min. [%min_ic%] bits)

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

JASPAR PBM Profiles

All profiles with a minimum specificity of bits (min. [%min_ic%] bits)

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

JASPAR PENDING Profiles

All profiles with a minimum specificity of bits (min. [%min_ic%] bits)

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

Custom Profiles

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%]%):
%

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.