Calculating the SNP-effective sample size from an alignment.
BACKGROUND
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.
Haubold
Bernhard
B
Max-Planck-Institut für Chemische Okologie, Carl-Zeiss-Promenade 10, D-07745 Jena, Germany.
Wiehe
Thomas
T
D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D030561:Databases, Nucleic Acid; D020224:Expressed Sequence Tags; D015894:Genome, Human; D006801:Humans; D051379:Mice; D020641:Polymorphism, Single Nucleotide; D018401:Sample Size; D016415:Sequence Alignment / Q000706:statistics & numerical data*; D012984:Software