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


CONCLUSIONS
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.
Lee
Hwan Young
HY
Department of Forensic Medicine, Yonsei University College of Medicine, Seoul, Korea. hylee192@yuhs.ac
Song
Injee
I
Ha
Eunho
E
Cho
Sung-Bae
SB
Yang
Woo Ick
WI
Shin
Kyoung-Jin
KJ
D001483:Base Sequence; D019295:Computational Biology / Q000379:methods*; D004272:DNA, Mitochondrial / Q000235:genetics*; D030541:Databases, Genetic; D006239:Haplotypes / Q000235:genetics; D020407:Internet; D019901:Locus Control Region / Q000235:genetics*; D008969:Molecular Sequence Data; D010802:Phylogeny; D012107:Research Design; D012984:Software
D004272:DNA, Mitochondrial