ProFASTA: a pipeline web server for fungal protein scanning with integration of cell surface prediction software

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/