PhaSePred

Predict the phase-separation propensity of a protein from its amino-acid sequence. Implementation of Chen et al. 2022 PNAS.

Install

pip install phasepred

Requires Python >= 3.12. The models and the DeepPhase table ship inside the package.

Four feature components cannot be redistributed and need a one-time install from the repository:

git clone https://github.com/notwhiteblank/PhaSePred.git && cd PhaSePred
bash tools/PScore/install.sh
bash tools/ESpritz/install.sh
bash tools/DeepCoil/install.sh
bash tools/PhosphoSitePlus/install.sh   # only needed for hSaPS / hPdPS

The installers put their data under ~/.local/share/phasepred/, where the package finds it automatically. phasepred check-tools prints a status row per component, and for every missing one the exact command that installs it. A complete install reports 9 OK.

Use

phasepred predict --fasta proteins.fasta --mode SaPS --output scores.csv

Four modes: SaPS and PdPS (any species, 8 features), hSaPS and hPdPS (human, 10 features). The output CSV carries the score plus every feature value.

Input can also be UniProt accessions:

phasepred predict --ids "P35637,Q9Y2W1" --mode SaPS --output scores.csv

More

Source, training data, retraining and AUC validation against the paper: https://github.com/notwhiteblank/PhaSePred