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Open Access Highly Accessed Software

mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences

Hwan Young Lee1, Injee Song2, Eunho Ha3, Sung-Bae Cho2, Woo Ick Yang1 and Kyoung-Jin Shin1*

Author Affiliations

1 Department of Forensic Medicine and Brain Korea 21 Project for Medical Science, Yonsei University College of Medicine, 250 Seongsanno, Seodaemun-gu, Seoul 120-752, Korea

2 Department of Computer Science, Yonsei University, 262 Seongsanno, Seodaemun-gu, Seoul 120-749, Korea

3 Department of Information and Statistics, Yonsei University, 234 Maeji-ri, Heungup-myun, Wounju-si, Gangwon-do 220-710, Korea

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BMC Bioinformatics 2008, 9:483  doi:10.1186/1471-2105-9-483

Published: 17 November 2008

Abstract

Background

For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny and referring to known mtDNA haplotypes can be useful for checking the quality of sequence data.

Results

We developed a Web-based bioinformatics resource "mtDNAmanager" that offers a convenient interface supporting the management and quality analysis of mtDNA sequence data. The mtDNAmanager performs computations on mtDNA control-region sequences to estimate the most-probable mtDNA haplogroups and retrieves similar sequences from a selected database. By the phased designation of the most-probable haplogroups (both expected and estimated haplogroups), mtDNAmanager enables users to systematically detect errors whilst allowing for confirmation of the presence of clear key diagnostic mutations and accompanying mutations. The query tools of mtDNAmanager also facilitate database screening with two options of "match" and "include the queried nucleotide polymorphism". In addition, mtDNAmanager provides Web interfaces for users to manage and analyse their own data in batch mode.

Conclusion

The mtDNAmanager will provide systematic routines for mtDNA sequence data management and analysis via easily accessible Web interfaces, and thus should be very useful for population, medical and forensic studies that employ mtDNA analysis. mtDNAmanager can be accessed at http://mtmanager.yonsei.ac.kr webcite.