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MITOMAP: a human mitochondrial genome database--1998 update

A. Kogelnik
1998 Nucleic Acids Research  
We have continued to develop MITOMAP (http://www.gen.emory.edu/MITOMAP ), a comprehensive database for the human mitochondrial DNA (mtDNA).  ...  Consequently, MITOMAP and GENOME provide a valuable reference for the mitochondrial biologist, in addition to being a model for the development of comprehensive, information storage and retrieval systems  ...  INTRODUCTION MITOMAP (1) is the most complete database of published data relating to the human mitochondrial genome.  ... 
doi:10.1093/nar/26.1.112 pmid:9399813 pmcid:PMC147233 fatcat:lj7had3difaqbf5ifxwm6cjfbq

Bioinformatics Tools and Databases to Assess the Pathogenicity of Mitochondrial DNA Variants in the Field of Next Generation Sequencing

Céline Bris, David Goudenege, Valérie Desquiret-Dumas, Majida Charif, Estelle Colin, Dominique Bonneau, Patrizia Amati-Bonneau, Guy Lenaers, Pascal Reynier, Vincent Procaccio
2018 Frontiers in Genetics  
The prioritization of mtDNA variants remains difficult, relying on a limited number of specific resources: population and clinical databases, and in silico tools providing a prediction of the variant pathogenicity  ...  genome.  ...  Hundreds of pathogenic mtDNA variants implicated in a variety of human diseases have now been reported in the continuously updated Human Mitochondrial Genome Database-the Mitomap (Ruiz-Pesini et al.,  ... 
doi:10.3389/fgene.2018.00632 pmid:30619459 pmcid:PMC6297213 fatcat:qufjegjoave27mmw325aywwmvu

Exaggerated status of "novel" and "pathogenic" mtDNA sequence variants due to inadequate database searches

Hans-Jürgen Bandelt, Antonio Salas, Robert W. Taylor, Yong-Gang Yao
2008 Human Mutation  
"Novelty" of a given mtDNA variant is most often equated with nonregistration in the extensive MITOMAP database (www.mitomap.org).  ...  with a disease case exhibiting clinical and biochemical features of mitochondrial dysfunction.  ...  R.W.T. thanks the Wellcome Trust, the Newcastle upon Tyne Hospitals Foundation NHS Trust, and the NHS NCG Rare Mitochondrial Disorders of Adults and Children Service) for their continuing financial support  ... 
doi:10.1002/humu.20846 pmid:18800376 fatcat:hthse4i4efb6jgge3h6fhe3acm

What is a 'novel' mtDNA mutation – and does 'novelty' really matter?

Hans-Jürgen Bandelt, Antonio Salas, Claudio M. Bravi
2006 Journal of Human Genetics  
database searches and straight forward Internet queries are carried out.  ...  The hunt for pathogenic mitochondrial DNA (mtDNA) mutations is often fueled by the seeming novelty of mutations that are either nonsynonymous or affect the protein synthesis machinery in patients.  ...  Note that this database was last updated 30 April 1998, and no new sequences are currently being added to it.  ... 
doi:10.1007/s10038-006-0066-5 pmid:17021933 fatcat:b6osxsjgf5bwfny45qmsghaxny

Genomic and Proteomic Databases and Applications: A Challenge for Database Technology [chapter]

Shamkant B. Navathe, Upen Patil
2004 Lecture Notes in Computer Science  
As an example, MITOMAP is a database documenting the human mitochondrial genome.  ...  MITOMAP is the most complete database of published data relating to the human mitochondrial genome.  ... 
doi:10.1007/978-3-540-24571-1_1 fatcat:kadmvkdkhfbo7kehclfugmiaku

Page 1373 of Cellular and Molecular Life Sciences Vol. 60, Issue 7 [page]

2003 Cellular and Molecular Life Sciences  
Chem. 22240-22250 Kogelnik A. M., Lott M. T., Brown M. D., Navathe S. B. and Wallace D. C. (1998) MITOMAP: a human mitochondrial genome database1998 update.  ...  T. (1996) Functional and molecular mi- tochondrial abnormalities associated with a C > T transition at position 3256 of the human mitochondrial genome.  ... 

"Mitochondrial Toolbox" – A Review of Online Resources to Explore Mitochondrial Genomics

Ruaidhri Cappa, Cassio de Campos, Alexander P. Maxwell, Amy J. McKnight
2020 Frontiers in Genetics  
There is emerging evidence that differences in the mitochondrial genome may contribute to multiple common diseases, leading to an increasing number of studies exploring mitochondrial genomics.  ...  Twenty-four online resources dedicated to mitochondrial genomics were reviewed.  ...  Database only Includes analytical tools MitoCarta 2.0 HmtDB MITOMAP Mitobreak MitoMiner 4.0 MSeqDr The mitochondrial proteome (IMPI) MtDNA-Server mtDB -Human Mitochondrial Genome Database  ... 
doi:10.3389/fgene.2020.00439 pmid:32457801 pmcid:PMC7225359 fatcat:fcnhcdwm5vdcdjd7e6ped53wpq

Mitochondrial DNA in human identification: a review

António Amorim, Teresa Fernandes, Nuno Taveira
2019 PeerJ  
based on sequences of the control region or full genomic sequences analysis is used to analyze a variety of forensic samples such as old bones, teeth and hair, as well as other biological samples where  ...  In this work we review mitochondrial DNA profiling methods used for human identification and present their use in the main cases of humanidentification focusing on the most relevant issues for forensics  ...  Another important human mtDNA database is Mitomap (Ruiz-Pesini et al., 2007) .  ... 
doi:10.7717/peerj.7314 pmid:31428537 pmcid:PMC6697116 fatcat:mzwucqoxrnd35d6uygugf4w6wm

Genomic and Proteomic Databases: Foundations, Current Status and Future Applications

Shamkant B. Navathe, Upen Patil, Wei Guan
2007 Journal of Computing Science and Engineering  
Two research case studies based on our own research are summarized dealing with the development of a new genome database called Mitomap and the creation of a framework for discovery of relationships among  ...  Whereas there are numerous databases related to various subfields of biology, we have maintained a focus on genomic and proteomic databases which are the crucial stepping stones for other fields and are  ...  As an example, MITOMAP is a database documenting the human mitochondrial genome.  ... 
doi:10.5626/jcse.2007.1.1.001 fatcat:sawebfga3bfybdibfq3yvhjf5u

Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation

Mannis van Oven, Manfred Kayser
2009 Human Mutation  
Although the phylogenetic resolution of global human mtDNA diversity has greatly improved as a result of increasing sequencing efforts of complete mtDNA genomes, an updated overall mtDNA tree is currently  ...  In order to facilitate a better use of known mtDNA variation, we have constructed an updated comprehensive phylogeny of global human mtDNA variation, based on both coding-and control region mutations.  ...  ACKNOWLEDGMENTS We thank the numerous colleagues who generated mtDNA sequence data and the NCBI GenBank database to make them publicly available.  ... 
doi:10.1002/humu.20921 pmid:18853457 fatcat:g6nkfi3dpfftxkt3thg7wpnhm4

Molecular Epidemiology of Mitochondrial Cardiomyopathy: A Search among Mitochondrial and Nuclear Genes

Cristina Mazzaccara, Bruno Mirra, Ferdinando Barretta, Martina Caiazza, Barbara Lombardo, Olga Scudiero, Nadia Tinto, Giuseppe Limongelli, Giulia Frisso
2021 International Journal of Molecular Sciences  
Mitochondrial Cardiomyopathy (MCM) is a common manifestation of multi-organ Mitochondrial Diseases (MDs), occasionally present in non-syndromic cases.  ...  in mitochondrial diseases.  ...  (ACMG) interpretations[120]and/or reported in MITOMAP (A Human Mitochondrial Genome Database.  ... 
doi:10.3390/ijms22115742 pmid:34072184 pmcid:PMC8197938 fatcat:kp2xjyht65dlffptcuucmkuk7y

A multi-parametric workflow for the prioritization of mitochondrial DNA variants of clinical interest

Mariangela Santorsola, Claudia Calabrese, Giulia Girolimetti, Maria Angela Diroma, Giuseppe Gasparre, Marcella Attimonelli
2015 Human Genetics  
Abstract Assigning a pathogenic role to mitochondrial DNA (mtDNA) variants and unveiling the potential involvement of the mitochondrial genome in diseases are challenging tasks in human medicine.  ...  Assuming that rare variants are more likely to be damaging, we designed a phylogenybased prioritization workflow to obtain a reliable pool of candidate variants for further investigations.  ...  The computational work has been executed on the IT resources made available by ReCaS, a project financed by the MIUR (Italian Ministry for Education, University and Research) in the "PON Ricerca e Competitività  ... 
doi:10.1007/s00439-015-1615-9 pmid:26621530 pmcid:PMC4698288 fatcat:kw7r53h3y5eelocpogm2z63gz4

Mitochondrial COX2 G7598A Mutation May Have a Modifying Role in the Phenotypic Manifestation of Aminoglycoside Antibiotic-Induced Deafness Associated with 12S rRNA A1555G Mutation in a Han Chinese Pedigree

Tianbin Chen, Qicai Liu, Ling Jiang, Can Liu, Qishui Ou
2013 Genetic Testing and Molecular Biomarkers  
The proband's complete mtDNA genome were amplified and direct sequencing was performed to determine the mitochondrial haplogroup and private mutations.  ...  The proband's mitochondrial haplogroup belonges to M7b1 and a private mutation MTCOX2 G7598A (p.Ala 5 Thr) is found.  ...  This work was supported by a grant from the National Science Fund (81041108) and Natural fund of Fujian Province (2012J01342).  ... 
doi:10.1089/gtmb.2012.0251 pmid:23256547 pmcid:PMC3552164 fatcat:2x5aox2cnvgxjltnz5yohmbtk4

Compilation of human mtDNA control region sequences

O Handt
1998 Nucleic Acids Research  
This paper describes the organisation of a database for human mitochondrial control-region sequences.  ...  ACKNOWLEDGEMENTS We are grateful to all colleagues who provided their sequence data as a computer file and gave additional information when needed.  ...  While we have collected only the control region sequences from humans there are other databases like MITOMAP (47) that collect information about the variabilitiy of the entire human mitochondrial genome  ... 
doi:10.1093/nar/26.1.126 pmid:9399816 pmcid:PMC147248 fatcat:7dv7ilqf6bat7kbpocwpo7llta

Phylogenetic Network and Physicochemical Properties of Nonsynonymous Mutations in the Protein-Coding Genes of Human Mitochondrial DNA

J. S. Moilanen
2003 Molecular biology and evolution  
We analyzed 840 complete coding-region human mitochondrial DNA (mtDNA) sequences for nonsynonymous mutations and evaluated the mutations in terms of the physicochemical properties of the amino acids involved  ...  The reduced-median networks of the amino acid changes revealed relatively few differences between the major continent-specific haplogroups, but a high variation and highly starlike phylogenies within the  ...  For these reasons, knowledge of the nature and phylogenetic relationships of amino acid haplotypes in the human mitochondrial genome is also important in clinical practice.  ... 
doi:10.1093/molbev/msg121 pmid:12777521 fatcat:py7tefnpwravlaqh3wv2e7ip3i
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