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

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...

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Bibliographic Details
Published in:	BMC bioinformatics Vol. 9; no. 1; p. 483
Main Authors:	Lee, Hwan Young, Song, Injee, Ha, Eunho, Cho, Sung-Bae, Yang, Woo Ick, Shin, Kyoung-Jin
Format:	Journal Article
Language:	English
Published:	England BioMed Central Ltd 17-11-2008 BioMed Central BMC
Subjects:	Base Sequence Computational Biology - methods Computer programs Databases, Genetic DNA, Mitochondrial - genetics Haplotypes - genetics Internet Locus Control Region - genetics Molecular Sequence Data Phylogeny Research Design Science Software
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Summary:	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. 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. 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.
Bibliography:	ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23
ISSN:	1471-2105 1471-2105
DOI:	10.1186/1471-2105-9-483