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Appears in Collections:Biological and Environmental Sciences Journal Articles
Peer Review Status: Refereed
Title: ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences
Author(s): Skeffington, Alastair W.
Donath, Andreas
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Keywords: General Agricultural and Biological Sciences
General Biochemistry, Genetics and Molecular Biology
General Medicine
General Neuroscience
Issue Date: 11-Sep-2020
Date Deposited: 4-Jul-2023
Citation: Skeffington AW & Donath A (2020) ProminTools: shedding light on proteins of unknown function in biomineralization with user friendly tools illustrated using mollusc shell matrix protein sequences. <i>PeerJ</i>, 8, Art. No.: e9852.
Abstract: Biominerals are crucial to the fitness of many organism and studies of the mechanisms of biomineralization are driving research into novel materials. Biomineralization is generally controlled by a matrix of organic molecules including proteins, so proteomic studies of biominerals are important for understanding biomineralization mechanisms. Many such studies identify large numbers of proteins of unknown function, which are often of low sequence complexity and biased in their amino acid composition. A lack of user-friendly tools to find patterns in such sequences and robustly analyse their statistical properties relative to the background proteome means that they are often neglected in follow-up studies. Here we present ProminTools, a user-friendly package for comparison of two sets of protein sequences in terms of their global properties and motif content. Outputs include data tables, graphical summaries in an html file and an R-script as a starting point for data-set specific visualizations. We demonstrate the utility of ProminTools using a previously published shell matrix proteome of the giant limpet Lottia gigantea.
DOI Link: 10.7717/peerj.9852
Rights: This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.
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