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bioRxiv · 10.1101/2023.12.19.572382

FastProtein: An automated software for in silico proteomic analysis

Moreira, R. S.·Filho, V. B.·Maia, G. A.·Soratto, T. A. T.·Kawagoe, E. K.·Russi, B. C.·Miletti, L. C.·Wagner, G.
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Abstract

BackgroundAlthough various tools provide proteomic information, each has its limitations regarding execution platforms, libraries, versions, and data output format. Therefore, integrating data analyses generated using different software programs is a manual process that can prolong the analysis time. ResultsThis paper presents FastProtein, a protein analysis pipeline tool developed in Java. This tool is user-friendly, easily installable, and provides important information regarding the subcellular location, transmembrane domains, signal peptide, molecular weight, isoelectric point, hydropathy, aromaticity, gene ontology, endoplasmic reticulum retention domains, and N- glycosylation domains of a protein. Furthermore, it helps determine the presence of glycosylphosphatidylinositol and obtain annotation information using InterProScan, PANTHER, PFam, and alignment-based annotation searches. Additionally, the software outputs a protein dataset with evidence of membrane localization. ConclusionsThe proposed tool provides the scientific community with an easy and user-friendly computational tool for proteomics data analysis. The tool is applicable to both small datasets and proteome-wide studies. It can be used in either the command line interface mode or through a web interface installed on a local server or via the BioLib web interface (http://biolib.com/UFSC/FastProtein). FastProtein also accelerates proteomics analysis routines by generating multiple results in a one-step run. The software is open-source and freely available. Installation and execution instructions, as well as the source code and test files generated for tool validation, are provided at https://github.com/bioinformatics-ufsc/FastProtein.

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Moreira, R. S., Filho, V. B., Maia, G. A., Soratto, T. A. T., Kawagoe, E. K., Russi, B. C., Miletti, L. C., Wagner, G.. 2023-12-20. FastProtein: An automated software for in silico proteomic analysis. https://doi.org/10.1101/2023.12.19.572382

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