is-pero

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is-pero is a tool designed for the prediction and classification of peroxisomal proteins. It utilizes advanced machine learning models and sequence analysis techniques to provide accurate and interpretable results. The server supports high-throughput proteomics studies by allowing batch predictions. The tools is available as web interface and for local runnin on GitHub and DockerHub

Server Input

is-pero webserver accepts in input protein sequences in FASTA format or providing UniProt IDs. Users can submit up to 100 protein sequences per job. These sequences can either be pasted directly into the input box or uploaded as a FASTA file. The web inteface allows to predict whether the submitted proteins are peroxisomal or not by selecting "Yes" among the Predict peroxisomal protein buttons. When this option is selected the downstream predictions are preformed only in the subset of proteins predicted as perxosomal. Alternativele when this prediction is not preformed the tool sonsiders all the proteins perosisomal and the downstream analisis is performed for all the sequences. Two example of inputs can be loaded through links included in the submission page.

Server Output

The is-pero webserver returns aggregated the results of three sequencial prediction steps:

• An optional step predicting if the input protein is peroxisomal or not.

• Predict if the protein is located matriax or the membran of the peroxisome.

• Detection of specific peptide signals PTS1, PTS2 and mPTS. For the selected membrane peptides (mPTS) the prediction of the bonding probabilities are returned.

Upon submission, is-pero processes the input and returns both a tabular output displayed with DataTables and downloadable CSV file containing detailed results. The output includes sequence IDs, localization probabilities, signal peptide matches, and predictions for MPTS regions if thery are retrieved by regular expressions. If the inital optional step, predicting peroxisomal protein, is not performed the corresponding probability for each protein of being peroxisomal is not displayed. In details the TSV output includes the following data:

• Sequence_ID: sequence identifier provided in the fasta file.

• Peroxisomal: yes or no (Optional)

• Probability_Peroxisomal: Probability of the sequence to be peroxisomal (Optional)

• Matrix: the subcellular localization of the peroxisomal protein is in matrix or membrane.

• Probability_Matrix: Probability of the sequence to be in the matrix of the peroxisome.

• Peptide: membrane peroxisomal targeting signal (MPTS) peptide detected by regular expression.

• Start: position of starting point in the MPTS peptide.

• Score: MPTS pattern matching score.

• Signal: membrane or other PTSs.

• Probability_MPTS: probability pf the peptiade to be MPTS.

This structured output allows easy interpretation and integration into further proteomics workflows. An example of output of the web interface if reported below.

Usage Notes

Ensure that all input sequences are in the correct FASTA format. Jobs may take longer to process if the maximum number of sequences (100) is submitted. For best results, review the mPTS predictions alongside other localization.

Contact

For additional support or inquiries, please contact Marco Anteghini or Emidio Capriotti .