Journal article
Efficient algorithms for counting and reporting segregating sites in genomic sequences
Journal of Computational Biology, Vol.14(7), pp.1001-1010
2007
Abstract
The number of segregating sites provides an indicator of the degree of DNA sequence variation that is present in a sample, and has been of great interest to the biological, pharmaceutical and medical professions. In this paper, we first provide linear- and expected-sublinear-time algorithms for finding all the segregating sites of a given set of DNA sequences. We also describe a data structure for tracking segregating sites in a set of sequences, such that every time the set is updated with the insertion of a new sequence or removal of an existing one, the segregating sites are updated accordingly without the need to re-scan the entire set of sequences.
Details
- Title
- Efficient algorithms for counting and reporting segregating sites in genomic sequences
- Authors/Creators
- M. Christodoulakis (Author/Creator)G.B. Golding (Author/Creator)C.S. Iliopoulos (Author/Creator)Y.J.P. Ardila (Author/Creator)W.F. Smyth (Author/Creator)
- Publication Details
- Journal of Computational Biology, Vol.14(7), pp.1001-1010
- Publisher
- Mary Ann Liebert Inc.
- Identifiers
- 991005545066807891
- Murdoch Affiliation
- Murdoch University
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 1 Clinical & Life Sciences
- 1.189 Genome Studies
- 1.189.310 Population Genetics
- Web Of Science research areas
- Biochemical Research Methods
- Biotechnology & Applied Microbiology
- Computer Science, Interdisciplinary Applications
- Mathematical & Computational Biology
- Statistics & Probability
- ESI research areas
- Biology & Biochemistry