299 517

Cited 59 times in

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

Authors
 Hwan Young Lee  ;  Injee Song  ;  Eunho Ha  ;  Sung-Bae Cho  ;  Woo Ick Yang  ;  Kyoung-Jin Shin 
Citation
 BMC BIOINFORMATICS, Vol.9 : 483, 2008 
Journal Title
BMC BIOINFORMATICS
Issue Date
2008
MeSH
Base Sequence ; Computational Biology/methods* ; DNA, Mitochondrial/genetics* ; Databases, Genetic* ; Haplotypes/genetics ; Internet* ; Locus Control Region/genetics* ; Molecular Sequence Data ; Phylogeny ; Research Design ; Software*
Keywords
Base Sequence ; Computational Biology/methods* ; DNA, Mitochondrial/genetics* ; Databases, Genetic* ; Haplotypes/genetics ; Internet* ; Locus Control Region/genetics* ; Molecular Sequence Data ; Phylogeny ; Research Design ; Software*
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
Files in This Item:
T200801643.pdf Download
DOI
10.1186/1471-2105-9-483
Appears in Collections:
1. College of Medicine (의과대학) > Dept. of Forensic Medicine (법의학과) > 1. Journal Papers
1. College of Medicine (의과대학) > Dept. of Pathology (병리학교실) > 1. Journal Papers
Yonsei Authors
Shin, Kyoung Jin(신경진) ORCID logo https://orcid.org/0000-0002-1059-9665
Yang, Woo Ick(양우익) ORCID logo https://orcid.org/0000-0002-6084-5019
Lee, Hwan Young(이환영)
URI
https://ir.ymlib.yonsei.ac.kr/handle/22282913/107980
사서에게 알리기
  feedback

qrcode

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

Browse

Links