Please use this identifier to cite or link to this item: https://doi.org/10.1093/bioinformatics/bth037
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dc.titleGood spaced seeds for homology search
dc.contributor.authorChoi, K.P.
dc.contributor.authorZeng, F.
dc.contributor.authorZhang, L.
dc.date.accessioned2014-10-28T02:50:06Z
dc.date.available2014-10-28T02:50:06Z
dc.date.issued2004-05-01
dc.identifier.citationChoi, K.P., Zeng, F., Zhang, L. (2004-05-01). Good spaced seeds for homology search. Bioinformatics 20 (7) : 1053-1059. ScholarBank@NUS Repository. https://doi.org/10.1093/bioinformatics/bth037
dc.identifier.issn13674803
dc.identifier.urihttp://scholarbank.nus.edu.sg/handle/10635/104495
dc.description.abstractMotivation: Filtration is an important technique used to speed up local alignment as exemplified in the BLAST programs. Recently, Ma et al. discovered that better filtering can be achieved by spacing out the matching positions according to a certain pattern, instead of contiguous positions to trigger a local alignment in their PatternHunter program. Such a match pattern is called a spaced seed. Results: Our numerical computation shows that the ranks of spaced seeds (based on sensitivity) change with the sequences similarity. Since homologous sequences may have diverse similarity, we assess the sensitivity of spaced seeds over a range of similarity levels and present a list of good spaced seeds for facilitating homology search in DNA genomic sequences. We validate that the listed spaced seeds are indeed more sensitive using three arbitrarily chosen pairs of DNA genomic sequences. © Oxford University Press 2004; all rights reserved.
dc.sourceScopus
dc.typeArticle
dc.contributor.departmentMATHEMATICS
dc.description.doi10.1093/bioinformatics/bth037
dc.description.sourcetitleBioinformatics
dc.description.volume20
dc.description.issue7
dc.description.page1053-1059
dc.description.codenBOINF
dc.identifier.isiut000221139700007
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