Select your input

Upload your sequences as a fasta file:

Or paste your fasta file here:

OR

Download SAPPHIRE

For sequences longer than 5k basepairs, it is advisable to download SAPPHIRE and run it locally.

Required python3 packages: numpy, keras, biopython
Usage: cd to SAPPHIRE directory
Run:
  python3 *SAPPHIRE version*.py input.fasta
Or (to include the reverse complements):
  python3 *SAPPHIRE version*.py -r input.fasta
Available SAPPHIRE versions: SAPPHIRE.py
SAPPHIRE_CNN_pseudomonas.py
SAPPHIRE_CNN_salmonella.py

References

SAPPHIRE

Coppens, L., & Lavigne, R. (2020). SAPPHIRE: a neural network based classifier for σ70 promoter prediction in Pseudomonas. In BMC Bioinformatics (Vol. 21, Issue 1). Springer Science and Business Media LLC. https://doi.org/10.1186/s12859-020-03730-z

SAPPHIRE.CNN

Coppens, L., Wicke, L., & Lavigne, R. (2022). SAPPHIRE.CNN: Implementation of dRNA-seq-driven, species-specific promoter prediction using convolutional neural networks. In Computational and Structural Biotechnology Journal (Vol. 20, pp. 4969–4974). Elsevier BV. https://doi.org/10.1016/j.csbj.2022.09.006