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Calculating the SNP-effective sample size from an alignment.

Bernhard Haubold·Thomas Wiehe
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Abstract

MOTIVATION: The number of Single Nucleotide Polymorphisms (SNPs) detectable in an alignment is a function of the length and the number of the aligned sequences. The latter is called sample size. However, a typical alignment, for instance obtained as a BLAST-search result of a query sequence against an EST database, does not evenly cover the query sequence. Therefore, it is usually not clear what the actual sample size is. RESULTS: We present a method to calculate the effective sample size, called n(eff), for a given BLAST alignment. This method takes into account that multiple coverage contributes only logarithmically to the SNP yield of a given sequence stretch. We show that the effective sample size n(eff) is usually much smaller than would be expected for a given amount of coverage and illustrate this with two typical examples.

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AlgorithmsAnimalsComputational BiologyDatabases, Nucleic AcidExpressed Sequence TagsGenome, HumanHumansMicePolymorphism, Single NucleotideSample SizeSequence AlignmentSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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Bernhard Haubold, Thomas Wiehe. 2002. Calculating the SNP-effective sample size from an alignment.. https://doi.org/10.1093/bioinformatics%2F18.1.36

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