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dc.contributor.authorCartwright, Reed A
dc.date.accessioned2013-06-12T15:21:22Z
dc.date.available2013-06-12T15:21:22Z
dc.date.issued2006-12-05
dc.identifier.citationBMC Bioinformatics. 2006 Dec 05;7(1):527
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2105-7-527
dc.identifier.urihttp://hdl.handle.net/10724/19785
dc.description.abstractAbstract Background Studies on the distribution of indel sizes have consistently found that they obey a power law. This finding has lead several scientists to propose that logarithmic gap costs, G (k) = a + c ln k, are more biologically realistic than affine gap costs, G (k) = a + bk, for sequence alignment. Since quick and efficient affine costs are currently the most popular way to globally align sequences, the goal of this paper is to determine whether logarithmic gap costs improve alignment accuracy significantly enough the merit their use over the faster affine gap costs. Results A group of simulated sequences pairs were globally aligned using affine, logarithmic, and log-affine gap costs. Alignment accuracy was calculated by comparing resulting alignments to actual alignments of the sequence pairs. Gap costs were then compared based on average alignment accuracy. Log-affine gap costs had the best accuracy, followed closely by affine gap costs, while logarithmic gap costs performed poorly. Subsequently a model was developed to explain the results. Conclusion In contrast to initial expectations, logarithmic gap costs produce poor alignments and are actually not implied by the power-law behavior of gap sizes, given typical match and mismatch costs. Furthermore, affine gap costs not only produce accurate alignments but are also good approximations to biologically realistic gap costs. This work provides added confidence for the biological relevance of existing alignment algorithms.
dc.titleLogarithmic gap costs decrease alignment accuracy
dc.typeJournal Article
dc.date.updated2013-06-07T19:29:52Z
dc.description.versionPeer Reviewed
dc.language.rfc3066en
dc.rights.holderReed A Cartwright et al.; licensee BioMed Central Ltd.


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