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Nucleic Acids Research 2005 33(Web Server Issue):W483-W488; doi:10.1093/nar/gki428
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© The Author 2005. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oupjournals.org

Article

SNPAnalyzer: a web-based integrated workbench for single-nucleotide polymorphism analysis

Jinho Yoo1, Bonghee Seo1 and Yangseok Kim1,2,*

1Bioinformatics Unit, ISTECH Inc. No. 506, Woongshin Art Plaza, 847 Janghang2-dong, Ilsan-gu, Goyang-si, Gyeonggi-do, 411-837, Republic of Korea 2Cancer Metastasis Research Center, Yonsei University College of Medicine 134 Shinchon-dong, Seodaemun-gu, Seoul 120-752, Republic of Korea

*To whom correspondence should be addressed. Tel: +82 31 9031155; Fax: +82 31 9031152; Email: yskim{at}istech21.com

Received January 19, 2005. Revised March 9, 2005. Accepted March 24, 2005.

SNPAnalyzer is a software that performs four essential statistical analyses of SNPs in a common computational environment. It is composed of three main modules: (i) data manipulation, (ii) analysis and (iii) visualization. The data manipulation module is responsible for data input and output, and handles genotype, phenotype and genetic distance data. To ensure user convenience, the data format is simple. The analysis module performs statistical calculations and consists of four subcomponents: (i) Hardy–Weinberg equilibrium, (ii) Haplotype Estimation, (iii) linkage disequilibrium (LD) and (iv) quantitative trait locus analysis. The main feature of the analysis module is multiple implementations of different algorithms and indices for haplotype estimation and for LD analysis. This enables users to compare separate results generated by different algorithms, which help to avoid biased results acquired by applying a single statistical algorithm. The performance of all implemented algorithms has been validated using experimentally proven datasets. The visualization module presents most of the analyzed results as figures, rather than as simple text, which aids in the intuitive understanding of complex data. The SNPAnalyzer has been developed using C and C++ and is available at http://www.istech.info/istech/board/login_form.jsp.


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