Campus Units
Computer Science
Document Type
Article
Publication Version
Published Version
Publication Date
2005
Journal or Book Title
BMC Bioinformatics
Volume
6
First Page
220
DOI
10.1186/1471-2105-6-220
Abstract
Background: The allele frequencies of single-nucleotide polymorphisms (SNPs) are needed to select an optimal subset of common SNPs for use in association studies. Sequence-based methods for finding SNPs with allele frequencies may need to handle thousands of sequences from the same genome location (sequences of deep coverage).
Results: We describe a computational method for finding common SNPs with allele frequencies in single-pass sequences of deep coverage. The method enhances a widely used program named PolyBayes in several aspects. We present results from our method and PolyBayes on eighteen data sets of human expressed sequence tags (ESTs) with deep coverage. The results indicate that our method used almost all single-pass sequences in computation of the allele frequencies of SNPs.
Conclusion: The new method is able to handle single-pass sequences of deep coverage efficiently. Our work shows that it is possible to analyze sequences of deep coverage by using pairwise alignments of the sequences with the finished genome sequence, instead of multiple sequence alignments.
Rights
This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
Copyright Owner
Wang and Huang
Copyright Date
2005
Language
en
File Format
application/pdf
Recommended Citation
Wang, Jianmin and Huang, Xiaoqiu, "A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage" (2005). Computer Science Publications. 32.
https://lib.dr.iastate.edu/cs_pubs/32
Comments
This article is published as Wang, Jianmin, and Xiaoqiu Huang. "A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage." BMC bioinformatics 6 (2005): 220. doi: 10.1186/1471-2105-6-220.