de.mpg.escidoc.pubman.appbase.FacesBean
English
 
Help Guide Disclaimer Contact us Login
  Advanced SearchBrowse

Item

ITEM ACTIONSEXPORT

Released

Journal Article

Calculating the SNP-effective sample size from an alignment

MPS-Authors
There are no MPG-Authors available
Locator
There are no locators available
Fulltext (public)
There are no public fulltexts available
Supplementary Material (public)
There is no public supplementary material available
Citation

Haubold, B., & Wiehe, T. (2002). Calculating the SNP-effective sample size from an alignment. Bioinformatics, 18(1), 36-38. doi:10.1093/bioinformatics/18.1.36.


Cite as: http://hdl.handle.net/11858/00-001M-0000-0010-0FCF-C
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.