Negative Set Generator Tool

This tools allows generation of a negative set to be compared with an experimental positive set of sequences using ROC-AUC tool. In all cases, the negative set has the same number of sequences of the original positive set and with the same nucleotide size. This is particularly important when using occupancy prediction. We offer two methods to generate a negative set :

  • “SUFFLE” This method randomly shuffle each sequence in the positive set of sequences so the new sequence has exactly the same proportion of the four nucleotides than the original positive sequence.
  • “GENOMIC” This method randomly select genomic regions that are not present in the positive set of sequences. This method requieres genomic information (chrosomome, position and size of each sequence in the positive set; see user guide for sequence’s name) and the nucleotide size of each chromosome (Give it as a list in a text file. Only numbers are allowed! Avoid using any other character; neither points or commas). It randomly generates a negative set of sequences that do not overlap with any sequence in the positive set.

Each method can have its advantage depending of the origin of the positive set and the porpose of the comparison.

This tool online has a limitation of 5 000 sequences or 10 000 000 of nucleotides for input alignment.

1. Input your data
Upload the positive sequence file :
(you can download an example here)

Method :

If you choose Genomic, upload the chromosome's size file :
(you can download an example here)
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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