[ HELP ]
Paste fasta formatted sequences (retrieve from Galaxy): OR upload a file containing a list of fasta formatted sequences:
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):
Choose a background (sequences randomly selected from experimental control peaks) [%FOREACH key = bg_seq_set_keys%] [%bg_seq_set_names.$key%] [%END%] 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
[%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:
All profiles with a minimum specificity of bits (min. [%min_ic%] bits) OR select specific profiles:
OR paste one or more TFBS profiles (retrieve from PAZAR or from JASPAR)
OR upload a file containing one or more TFBS profiles
Matrix match threshold (min. [%min_threshold%]%): % Number of results to display: Top 5 10 20 All results OR only results with Z-score >= [%FOREACH cutoff = zcutoffs%] [%cutoff%] [%END%] and Fisher score >= [%FOREACH cutoff = fcutoffs%] [%cutoff%] [%END%] and KS score >= [%FOREACH cutoff = kscutoffs%] [%cutoff%] [%END%] (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.