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How to:Calling SNPs without a reference sequence  

2011-03-26 20:06:03|  分类: 生物信息分析 |  标签: |举报 |字号 订阅

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Background

The most common application for the next-generation sequencing technologies is resequencing, where short reads from the genome of an individual are aligned to a reference genome sequence for the same species. These mappings can then be used to identify genetic differences among individuals in a population, and perhaps ultimately to explain phenotypic variation. Many algorithms capable of aligning short reads to the reference, and determining differences between them have been reported. Much less has been reported on how to use these technologies to determine genetic differences among individuals of a species for which a reference sequence is not available, which drastically limits the number of species that can easily benefit from these new technologies.

Results

We describe a computational pipeline, called DIAL (De novo Identification of Alleles), for identifying single-base substitutions between two closely related genomes without the help of a reference genome. The method works even when the depth of coverage is insufficient for de novo assembly, and it can be extended to determine small insertions/deletions. We evaluate the software's effectiveness using published Roche/454 sequence data from the genome of Dr. James Watson (to detect heterozygous positions) and recent Illumina data from orangutan, in each case comparing our results to those from computational analysis that uses a reference genome assembly. We also illustrate the use of DIAL to identify nucleotide differences among transcriptome sequences.

Conclusions

DIAL can be used for identification of nucleotide differences in species for which no reference sequence is available. Our main motivation is to use this tool to survey the genetic diversity of endangered species as the identified sequence differences can be used to design genotyping arrays to assist in the species' management. The DIAL source code is freely available at http://www.bx.psu.edu/miller_lab/ webcite.

Calling SNPs without a reference sequence

Aakrosh Ratan1 email, Yu Zhang1 email, Vanessa M Hayes2 email, Stephan C Schuster1 email and Webb Miller1 email

Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, USA

Children's Cancer Institute Australia for Medical Research, University of New South Wales, Randwick, Australia

How to:Calling SNPs without a reference sequence - 喜欢吃桃子 - wangyufeng的博客 author emailHow to:Calling SNPs without a reference sequence - 喜欢吃桃子 - wangyufeng的博客 corresponding author email

BMC Bioinformatics 2010, 11:130doi:10.1186/1471-2105-11-130

The electronic version of this article is the complete one and can be found online at: http://www.biomedcentral.com/1471-2105/11/130

Received: 31 August 2009
Accepted: 15 March 2010
Published: 15 March 2010

? 2010 Ratan et al; licensee BioMed Central Ltd.
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.

more information links to:http://www.biomedcentral.com/1471-2105/11/130

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