Objective Functions

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dc.authoridDogan, Haluk/0000-0002-6547-6638|Otu, Hasan/0000-0002-9253-8152
dc.authorwosidDogan, Haluk/AAH-3873-2020
dc.contributor.authorDogan, Haluk
dc.contributor.authorOtu, Hasan H.
dc.coverage.doi10.1007/978-1-62703-646-7
dc.date.accessioned2024-07-18T20:40:04Z
dc.date.available2024-07-18T20:40:04Z
dc.date.issued2014
dc.departmentİstanbul Bilgi Üniversitesien_US
dc.description.abstractMultiple sequence alignment involves alignment of more than two sequences and is an NP-complete problem. Therefore, heuristic algorithms that use different criteria to find an approximation to the optimal solution are employed. At the heart of these approaches lie the scoring and objective functions that a given algorithm uses to compare competing solutions in constructing a multiple sequence alignment. These objective functions are often motivated by the biological paradigms that govern functional similarities and evolutionary relations. Most existing approaches utilize a progressive process where the final alignment is constructed sequentially by adding new sequences into an existing multiple sequence alignment matrix, which is dynamically updated. In doing this, the core scoring function to assess accuracies of pairwise alignments generally remains the same, while the objective functions used in intermediary steps differ. Nevertheless, the overall assessment of the final multiple sequence alignment is generally calculated by an extension of pairwise scorings. In this chapter, we explore different scoring and objective functions used in calculating the accuracy and optimization of a multiple sequence alignment and provide utilization of these criteria in popularly used multiple sequence alignment algorithms.en_US
dc.identifier.doi10.1007/978-1-62703-646-7_3
dc.identifier.endpage58en_US
dc.identifier.isbn978-1-62703-645-0
dc.identifier.isbn978-1-62703-646-7
dc.identifier.issn1064-3745
dc.identifier.pmid24170394en_US
dc.identifier.scopus2-s2.0-84934443068en_US
dc.identifier.scopusqualityQ3en_US
dc.identifier.startpage45en_US
dc.identifier.urihttps://doi.org/10.1007/978-1-62703-646-7_3
dc.identifier.urihttps://hdl.handle.net/11411/6957
dc.identifier.volume1079en_US
dc.identifier.wosWOS:000328376500004en_US
dc.identifier.wosqualityN/Aen_US
dc.indekslendigikaynakWeb of Scienceen_US
dc.indekslendigikaynakScopusen_US
dc.indekslendigikaynakPubMeden_US
dc.language.isoenen_US
dc.publisherHumana Press Incen_US
dc.relation.ispartofMultiple Sequence Alignment Methodsen_US
dc.relation.publicationcategoryKitap Bölümü - Uluslararasıen_US
dc.rightsinfo:eu-repo/semantics/closedAccessen_US
dc.subjectScoring-Functionsen_US
dc.subjectScoring-Matricesen_US
dc.subjectSum-Of-Pairsen_US
dc.subjectProgressive-Alignmenten_US
dc.subjectConsistency-Based-Scoringen_US
dc.subjectMultiple Sequence Alignmenten_US
dc.subjectGap Penaltiesen_US
dc.subjectMafften_US
dc.subjectAccuracyen_US
dc.titleObjective Functions
dc.typeBook Chapter

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