Occupancy

This tool calculates Transcription Factor Occupancy as the relative expected number of bound transcription factor molecules (Roider et al., 2007) of each DNA sequence.

  • Option “All” use all sites in each sequence for Occupancy calculation. In this case, you can work with a maximum of 5000 DNA sequences and a maximum of 10 000 000 nucleotides.
  • Option “Limit” gives similar results than “All“ but a score limit can be specified so all sites with score worse than the limit will not be used. In this case, you can work with a maximum of 5000 DNA sequences and a maximum of 10 000 000 nucleotides.

This tool also gives a graphic output showing occupancy of each sequence and a histogram of occupancy distribution. The Result file can be used as input for ROC-AUC tool.

    

1. Input your data
Upload the matrix file :
(you can download an example here)
Upload a sequence file in fasta format :
(you can download an example here)
Option :
If you choose "limit", indicate its value :
Protein concentration :
2. Getting results
Enter a valid e-mail address where we can send a link to the results when the run is completed.
E-mail :  

 

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