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Updated: May 26, 2026
An Integrated Approach for Microprotein Identification and Sequence Analysis
Published on: July 12, 2022
ProFASTA: a pipeline web server for fungal protein scanning with integration of cell surface prediction software
Piet W J de Groot1, Bernd W Brandt
1Regional Center for Biomedical Research, Albacete Science and Technology Park, University of Castilla - La Mancha, 02006 Albacete, Spain. Piet.deGroot@uclm.es
Abstract:
Surface proteins, such as those located in the cell wall of fungi, play an important role in the interaction with the surrounding environment. For instance, they mediate primary host-pathogen interactions and are crucial to the establishment of biofilms and fungal infections. Surface localization of proteins is determined by specific sequence features and can be predicted by combining different freely available web servers. However, user-friendly tools that allow rapid analysis of large datasets (whole proteomes or larger) in subsequent analyses were not yet available. Here, we present the web tool ProFASTA, which integrates multiple tools for rapid scanning of protein sequence properties in large datasets and returns sequences in FASTA format. ProFASTA also allows for pipeline filtering of proteins with cell surface characteristics by analysis of the output created with SignalP, TMHMM and big-PI. In addition, it provides keyword, iso-electric point, composition and pattern scanning. Furthermore, ProFASTA contains all fungal protein sequences present in the NCBI Protein database. As the full fungal NCBI Taxonomy is included, sequence subsets can be selected by supplying a taxon name. The usefulness of ProFASTA is demonstrated here with a few examples; in the recent past, ProFASTA has already been applied successfully to the annotation of covalently-bound fungal wall proteins as part of community-wide genome annotation programs. ProFASTA is available at: http://www.bioinformatics.nl/tools/profasta/.
Insights
ProFASTA is a new web tool for analyzing fungal surface proteins. It rapidly scans large datasets, aiding in the study of fungal infections and biofilm formation.
Area of Science:
- Mycology
- Bioinformatics
- Computational Biology
Background:
- Fungal surface proteins, particularly in the cell wall, are critical for host-pathogen interactions, biofilm formation, and fungal infections.
- Predicting surface protein localization typically involves combining multiple web servers, which can be cumbersome for large-scale analyses.
- A need exists for user-friendly tools capable of rapid analysis of extensive protein datasets.
Purpose of the Study:
- To introduce ProFASTA, a novel web tool designed for the rapid scanning of protein sequence properties in large datasets.
- To enable efficient filtering of fungal proteins with cell surface characteristics.
- To provide a comprehensive resource for fungal protein analysis, including sequence properties and taxonomic filtering.
Main Methods:
- ProFASTA integrates multiple prediction tools (SignalP, TMHMM, big-PI) for analyzing protein sequences.
- It supports rapid scanning of protein sequence properties and keyword, isoelectric point, composition, and pattern analysis.
- The tool incorporates the entire fungal protein database from NCBI and the NCBI Taxonomy for subset selection.
Main Results:
- ProFASTA facilitates rapid scanning and filtering of large fungal proteomes for cell surface proteins.
- The tool returns analyzed sequences in FASTA format, streamlining downstream analyses.
- It allows users to select specific fungal subsets based on taxonomic classification.
Conclusions:
- ProFASTA offers a user-friendly and efficient solution for analyzing fungal surface proteins in large datasets.
- The tool has been successfully applied in genome annotation projects, demonstrating its practical utility.
- ProFASTA is a valuable resource for researchers studying fungal biology, pathogenesis, and host interactions.
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