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A Characteristic-Based Framework for Multiple Sequence Aligners

2018-01Artigo científico Acesso aberto
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dc.contributor.authorRubio-Largo, Álvaro
dc.contributor.authorVanneschi, Leonardo
dc.contributor.authorCastelli, Mauro
dc.contributor.authorVega-Rodriguez, Miguel A.
dc.contributor.institutionNOVA Information Management School (NOVA IMS)
dc.contributor.institutionInformation Management Research Center (MagIC) - NOVA Information Management School
dc.contributor.pblInstitute of Electrical and Electronics Engineers (IEEE)
dc.date.accessioned2022-12-22T22:09:31Z
dc.date.available2022-12-22T22:09:31Z
dc.date.issued2018-01
dc.descriptionRubio-Largo, Á., Vanneschi, L., Castelli, M., & Vega-Rodriguez, M. A. (2018). A Characteristic-Based Framework for Multiple Sequence Aligners. IEEE Transactions on Cybernetics, 48(1), 41-51. DOI: 10.1109/TCYB.2016.2621129 ---%ABS3%
dc.description.abstractThe multiple sequence alignment is a well-known bioinformatics problem that consists in the alignment of three or more biological sequences (protein or nucleic acid). In the literature, a number of tools have been proposed for dealing with this biological sequence alignment problem, such as progressive methods, consistency-based methods, or iterative methods; among others. These aligners often use a default parameter configuration for all the input sequences to align. However, the default configuration is not always the best choice, the alignment accuracy of the tool may be highly boosted if specific parameter configurations are used, depending on the biological characteristics of the input sequences. In this paper, we propose a characteristic-based framework for multiple sequence aligners. The idea of the framework is, given an input set of unaligned sequences, extract its characteristics and run the aligner with the best parameter configuration found for another set of unaligned sequences with similar characteristics. In order to test the framework, we have used the well-known multiple sequence comparison by log-expectation (MUSCLE) v3.8 aligner with different benchmarks, such as benchmark alignments database v3.0, protein reference alignment benchmark v4.0, and sequence alignment benchmark v1.65. The results shown that the alignment accuracy and conservation of MUSCLE might be greatly improved with the proposed framework, specially in those scenarios with a low percentage of identity. The characteristic-based framework for multiple sequence aligners is freely available for downloading at http://arco.unex.es/arl/fwk-msa/cbf-msa.zipen
dc.description.versionauthorsversion
dc.description.versionpublished
dc.format.extent10
dc.format.extent2092464
dc.identifier.doi10.1109/TCYB.2016.2621129
dc.identifier.issn2168-2267
dc.identifier.otherPURE: 3236493
dc.identifier.otherPURE UUID: 7d73807d-1098-46fc-875e-833b5e19a31c
dc.identifier.otherScopus: 84994323892
dc.identifier.otherWOS: 000418291400004
dc.identifier.otherORCID: /0000-0002-8793-1451/work/72856184
dc.identifier.otherORCID: /0000-0003-4732-3328/work/151426683
dc.identifier.urihttp://hdl.handle.net/10362/146530
dc.identifier.urlhttps://www.scopus.com/pages/publications/84994323892
dc.language.isoeng
dc.peerreviewedyes
dc.subjectCharacteristics-based
dc.subjectMultiple sequence alignment (MSA)
dc.subjectParticle swarm optimization (PSO)
dc.subjectControl and Systems Engineering
dc.subjectSoftware
dc.subjectInformation Systems
dc.subjectHuman-Computer Interaction
dc.subjectComputer Science Applications
dc.subjectElectrical and Electronic Engineering
dc.subjectSDG 3 - Good Health and Well-being
dc.titleA Characteristic-Based Framework for Multiple Sequence Alignersen
dc.typejournal article
degois.publication.firstPage41
degois.publication.issue1
degois.publication.lastPage51
degois.publication.titleIEEE Transactions on Cybernetics
degois.publication.volume48
dspace.entity.typePublication
rcaap.rightsopenAccess

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