Binding sequences

Select how binding sequences will be provided. If BED file is selected, a target species and assembly must be selected as well.

Background sequences

Select how background sequences should be generated.

  • If FASTA file is selected a FASTA file containing sequences must be provided.
  • If Generate from BED file is selected sequences will be generated from the provided BED file containing binding sequences.
  • If Shuffle input is selected sequences will be generated by reshuffling the provided binding sequences.

Sequence preprocessing

  • Min. sequence length: all sequences shorter than this will be discarded.
  • Max. sequence length: all sequences longer than this will be discarded.
  • BED file only: If Pad sequences is given all sequences will be padded with this number of surrounding bases.
  • BED file only: If Fixed sequence width is given all sequences will be trimmed/padded to fit this length.

Data split

Specify how sequences should be split for training, validation and testing.

Program control

Training model

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Model summary

Foreground sequences Background sequences

ROC curve

CNN filters ranked by score

Prediction score distribution

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Use example sequences
Predict paired sequences
Use example sequences
Enable long sequence prediction mode.


Plot profile difference (with variants only)
Download profile plots Download profile data
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deepclip-shiny version 0.1