Version 3.0

Sequence-based Anchored Combination Site Analysis

Select Analysis Parameters

[ 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:

vertebrate / insect / nematode / fungi

OR paste a TFBS profile (retrieve from PAZAR)

OR upload a file containing a TFBS profile

Select TFs to find in combination with anchoring TF

All JASPAR CORE profiles from the following tax groups:
  vertebrates   insects   nematodes   fungi
  with a minimum specificity of  bits (min. 8 bits)

OR select specific profiles:

vertebrates insects nematodes fungi

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

OR upload a file containing one or more TFBS profiles


STEP 4: Select parameters

[ HELP ]

Matrix match threshold (min. 75%):
%

Maximum inter-binding distance (max. = 250)

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.