Effect of the sequence data deluge on the performance of methods for detecting protein functional residues

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• dc.contributor.author Garrido Martín, Diego, 1992-
• dc.contributor.author Pazos, Florencio
• dc.date.accessioned 2019-05-31T07:29:45Z
• dc.date.available 2019-05-31T07:29:45Z
• dc.date.issued 2018
• dc.description.abstract Background: The exponential accumulation of new sequences in public databases is expected to improve the performance of all the approaches for predicting protein structural and functional features. Nevertheless, this was never assessed or quantified for some widely used methodologies, such as those aimed at detecting functional sites and functional subfamilies in protein multiple sequence alignments. Using raw protein sequences as only input, these approaches can detect fully conserved positions, as well as those with a family-dependent conservation pattern. Both types of residues are routinely used as predictors of functional sites and, consequently, understanding how the sequence content of the databases affects them is relevant and timely. Results: In this work we evaluate how the growth and change with time in the content of sequence databases affect five sequence-based approaches for detecting functional sites and subfamilies. We do that by recreating historical versions of the multiple sequence alignments that would have been obtained in the past based on the database contents at different time points, covering a period of 20 years. Applying the methods to these historical alignments allows quantifying the temporal variation in their performance. Our results show that the number of families to which these methods can be applied sharply increases with time, while their ability to detect potentially functional residues remains almost constant. Conclusions: These results are informative for the methods’ developers and final users, and may have implications in the design of new sequencing initiatives.
• dc.description.sponsorship This work was partially funded by the Spanish Ministry for Economy and Competitiveness [SAF2016–78041-C2–2-R to F.P.]. The work of D.G.M. was supported by a scholarship from the XIII Certamen Universitario Arquimedes (Spanish Ministry for Education, Culture and Sports).
• dc.format.mimetype application/pdf
• dc.identifier.citation Garrido-Martín D, Pazos F. Effect of the sequence data deluge on the performance of methods for detecting protein functional residues. BMC Bioinformatics. 2018; 19(1):67. DOI 10.1186/s12859-018-2084-7
• dc.identifier.doi http://dx.doi.org/10.1186/s12859-018-2084-7
• dc.identifier.issn 1471-2105
• dc.identifier.uri http://hdl.handle.net/10230/41677
• dc.language.iso eng
• dc.publisher BioMed Central
• dc.relation.ispartof BMC Bioinformatics. 2018; 19(1):67
• dc.relation.projectID info:eu-repo/grantAgreement/ES/1PE/SAF2016–78041-C2–2-R
• dc.rights © The Author(s). 2018 Open Access This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
• dc.rights.accessRights info:eu-repo/semantics/openAccess
• dc.rights.uri http://creativecommons.org/licenses/by/4.0/
• dc.subject.keyword Conserved positions
• dc.subject.keyword Family-dependent conserved position
• dc.subject.keyword Functional residue
• dc.subject.keyword Functional subfamily
• dc.subject.keyword Sequence database
• dc.subject.keyword Specificity-determining position
• dc.title Effect of the sequence data deluge on the performance of methods for detecting protein functional residues
• dc.type info:eu-repo/semantics/article
• dc.type.version info:eu-repo/semantics/publishedVersion