mtDNA Variation and Analysis Using Mitomap and Mitomaster

Marie T Lott; Jeremy N Leipzig; Olga Derbeneva; H Michael Xie; Dimitra Chalkia; Mahdi Sarmady; Vincent Procaccio; Douglas C Wallace

doi:10.1002/0471250953.bi0123s44

mtDNA Variation and Analysis Using Mitomap and Mitomaster

Curr Protoc Bioinformatics. 2013 Dec;44(123):1.23.1-26. doi: 10.1002/0471250953.bi0123s44.

Authors

Marie T Lott¹, Jeremy N Leipzig², Olga Derbeneva³, H Michael Xie⁴, Dimitra Chalkia⁵, Mahdi Sarmady⁶, Vincent Procaccio⁷, Douglas C Wallace⁸

Affiliations

¹ Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, Pennsylvania, USA.
² Center for Biomedical Informatics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; phone: 1-267-426-1375; fax: 1-215-590-5245.
³ Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; phone: 1-267-425-3064; fax: 1-267-426-0978; work cell: 1-215-866-8121.
⁴ Center for Biomedical Informatics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; phone: 1-267-426-0675; fax: 1-215-590-5245.
⁵ Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA.
⁶ Center for Biomedical Informatics, The Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; phone: 1-267-426-1373; fax: 1-215-590-5245.
⁷ National Center for Neurodegenerative and Mitochondrial Diseases CHU Angers, Biochemistry and Genetics Department, Angers, France.
⁸ Center for Mitochondrial and Epigenomic Medicine, Children's Hospital of Philadelphia Research Institute, Philadelphia, PA; Department of Pathology and Laboratory Medicine; University of Pennsylvania, Philadelphia, PA; phone: 1-267-425-3078; fax: 1-267-426-0978.

Abstract

The Mitomap database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians and genetic counselors for the past twenty-five years. The Mitomap protocol shows how users may look up human mitochondrial gene loci, search for public mitochondrial sequences, and browse or search for reported general population nucleotide variants as well as those reported in clinical disease. Within Mitomap is the powerful sequence analysis tool for human mitochondrial DNA, Mitomaster. The Mitomaster protocol gives step-by-step instructions showing how to submit sequences to identify nucleotide variants relative to the rCRS, to determine the haplogroup, and to view species conservation. User-supplied sequences, GenBank identifiers and single nucleotide variants may be analyzed.

Keywords: GenBank sequences; biological database; haplogroups; human mitochondrial DNA; information retrieval; single nucleotide variants; species conservation.

Publication types

Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Base Sequence
DNA, Mitochondrial / genetics*
Databases, Genetic*
Genetic Code
Genetic Variation*
Haplotypes / genetics
Humans
Molecular Sequence Data
Polymorphism, Restriction Fragment Length
Polymorphism, Single Nucleotide / genetics
Sequence Alignment
Software*

Substances

DNA, Mitochondrial

Abstract

Publication types

MeSH terms

Substances

Grants and funding