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

Hwan Young Lee,Sung-Bae Cho,Woo Ick Yang,Kyoung-Jin Shin,Injee Song,Eunho Ha

doi:10.1186/1471-2105-9-483

Abstract

BackgroundFor 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.ResultsWe 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.ConclusionThe 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 .

Highlights

For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA data
Refinement of mitochondrial DNA (mtDNA) phylogeny with more diagnostic mutations would facilitate the detection of more errors in mtDNA sequence data since it is based on mutation motifs, and if haplogroup determination fails, a neighbourhood search for sequences in the available database could identify a subset of potentially closely related sequences, thereby allowing researchers to pinpoint errors in the sequence by comparing the sequence in question with a limited subset of the total database [4]
With the alternative setting of match, mtDNAmanager searches sequences that match the queried sequence data from the database. mtDNAmanager provides match options to select specific regions to be analysed [HV1: np 16024–16365; HV2: np 73–340; HV3: np 438–576; and control-region: np 16024–16569, np 1–576], ignore heteroplasmic insertions in poly C-stretches and permit mismatches in order to overcome differences in data reporting between laboratories due to variability in the analysis region, ambiguities with respect to mtDNA nomenclature and different treatment of length variants

Summary

Introduction

For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. For the past few years, scientific controversy has surrounded the large numbers of errors detected in much of the previously published mtDNA data [1,2]. Refinement of mtDNA phylogeny with more diagnostic mutations would facilitate the detection of more errors in mtDNA sequence data since it is based on mutation motifs, and if haplogroup determination fails, a neighbourhood search for sequences in the available database could identify a subset of potentially closely related sequences, thereby allowing researchers to pinpoint errors in the sequence by comparing the sequence in question with a limited subset of the total database [4]. Manual haplogroup estimation requires a thorough understanding of the worldwide mtDNA phylogeny, and database screening for systematic error detection requires high-quality databases that are publicly available

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