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  Aligment-free population genomics: an efficient estimator of sequence diversity

Haubold, B., & Pfaffelhuber, P. (2012). Aligment-free population genomics: an efficient estimator of sequence diversity. G3: Genes, Genomes, Genetics, 2(8), 883-889. doi:10.1534/g3.112.002527.

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Item Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-7E8C-C Version Permalink: http://hdl.handle.net/11858/00-001M-0000-000E-7E8D-A
Genre: Journal Article

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Haubold_2012.pdf (Publisher version), 831KB
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 Creators:
Haubold, Bernhard1, Author              
Pfaffelhuber, Peter, Author
Affiliations:
1Research Group Bioinformatics, Department Evolutionary Genetics, Max Planck Institute for Evolutionary Biology, Max Planck Society, escidoc:1445644              

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Free keywords: genetic diversity; alignment-free; maximumlikelihood; Drosophila; match length; distribution
 Abstract: Comparative sequencing contributes critically to the functional annotation of genomes. One prerequisite for successful analysis of the increasingly abundant comparative sequencing data is the availability of efficient computational tools. We present here a strategy for comparing unaligned genomes based on a coalescent approach combined with advanced algorithms for indexing sequences. These algorithms are particularly efficient when analyzing large genomes, as their run time ideally grows only linearly with sequence length. Using this approach, we have derived and implemented a maximumlikelihood estimator of the average number of mismatches per site between two closely related sequences, p. By allowing for fluctuating coalescent times, we are able to improve a previously published alignment-free estimator of p. We show through simulation that our new estimator is fast and accurate even with moderate recombination (r # p). To demonstrate its applicability to real data, we compare the unaligned genomes of Drosophila persimilis and D. pseudoobscura. In agreement with previous studies, our sliding window analysis locates the global divergence minimum between these two genomes to the pericentromeric region of chromosome 3.

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Language(s): eng - English
 Dates: 2012-08
 Publication Status: Published in print
 Pages: -
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 Table of Contents: -
 Rev. Method: -
 Identifiers: DOI: 10.1534/g3.112.002527
Other: 2969/S 39314
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Title: G3: Genes, Genomes, Genetics
Source Genre: Journal
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Publ. Info: Genetics Society of America
Pages: - Volume / Issue: 2 (8) Sequence Number: - Start / End Page: 883 - 889 Identifier: ISSN: 2160-1836