PROSITE Signature Finder

A simple Python script to detect PROSITE-like motifs in protein sequences (FASTA format) using Biopython library. This project demonstrates the use of regular expressions and Biopython to locate biologically meaningful sequence patterns; shown here using a real example related to the ProSeC project at Forschungszentrum Jülich.

Purpose:

• Reading and parsing FASTA files with Biopython

• Searching for PROSITE-style sequence motifs with regular expressions

• Applying a biologically meaningful motif (A-x-A) linked to protein secretion in Corynebacterium glutamicum

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How to run

Requirements:

• Python 3.8+
• Biopython. Install with this line:

pip install biopython

To run the file:

python prosite_regex_find.py

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Modules used

This program relies on two main modules:

• re: handles regular expressions and used to search for motifs.
• Bio.SeqIO: reads and parses FASTA files, giving access to sequence IDs and amino acids strings.

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Example: Signal Peptide Motif in Corynebacterium glutamicum

The example sequence used here is the putative L,D-transpeptidase LppS (UniProt ID: Q8NMT9) from Corynebacterium glutamicum, the model organism used in the ProSeC project for studying protein secretion via the Sec pathway.

A characteristic sequence element of Sec-type signal peptides is the A-x-A motif (A = Alanine, x = any amino acid).

It represents the (–3, –1) rule at the cleavage site where the signal peptidase cuts the peptide before export, a feature described in:

• von Heijne G. (1983) Patterns of amino acids near signal-sequence cleavage sites. (DOI)

• PROSITE entry PS00013 (Signal peptide cleavage site).

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Example input/output

1) Occurences found

• Enter the signature: A.{1}A
• Enter the path of your FASTA file.
• The output would be:

2) Occurences not found