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MITOMAP: an update on the status of the human mitochondrial genome database

A. M. Kogelnik, M. T. Lott, M. D. Brown, S. B. Navathe, D. C. Wallace
1997 Nucleic Acids Research  
This paper is an update of the changes which have occurred to MITOMAP over the past year.  ...  We have continued to develop MITOMAP, a comprehensive database for the human mitochondrial DNA (mtDNA).  ...  INTRODUCTION MITOMAP (1) is a database of all published data relating to the human mitochondrial genome.  ... 
doi:10.1093/nar/25.1.196 pmid:9016535 pmcid:PMC146395 fatcat:adyukfqibrhe3k4zhyjobylrne

A comprehensive collection of annotations to interpret sequence variation in human mitochondrial transfer RNAs

Maria Angela Diroma, Paolo Lubisco, Marcella Attimonelli
2016 BMC Bioinformatics  
The abundance of biological data characterizing the genomics era is contributing to a comprehensive understanding of human mitochondrial genetics.  ...  and prioritization available so far cannot shed light on the functional role of tRNA variations.  ...  Acknowledgements The authors would like to thank Dr Claudia Calabrese, Dr Domenico Simone and Dr Mariangela Santorsola, co-developers of the MToolBox pipeline, for helpful Competing interests The authors  ... 
doi:10.1186/s12859-016-1193-4 pmid:28185569 pmcid:PMC5123245 fatcat:kp664u567vesxax4scha3kc754

HmtDB, a genomic resource for mitochondrion-based human variability studies

Francesco Rubino, Roberta Piredda, Francesco Maria Calabrese, Domenico Simone, Martin Lang, Claudia Calabrese, Vittoria Petruzzella, Mila Tommaseo-Ponzetta, Giuseppe Gasparre, Marcella Attimonelli
2011 Nucleic Acids Research  
The database hosts human mitochondrial genome sequences annotated with population and variability data, the latter being estimated through the application of the SiteVar software based on site-specific  ...  Classifier tools implemented in HmtDB allow the prediction of the haplogroup for any human mitochondrial genome currently stored in HmtDB or externally submitted de novo by an end-user.  ...  The maintenance and updating of the database is possible thanks to the voluntary contribution of students and young graduates.  ... 
doi:10.1093/nar/gkr1086 pmid:22139932 pmcid:PMC3245114 fatcat:ktfanwoa5jehnh7ntndaj4pmpa

MitoTool: A web server for the analysis and retrieval of human mitochondrial DNA sequence variations

Long Fan, Yong-Gang Yao
2011 Mitochondrion (Amsterdam. Print)  
Furthermore, it offers an integrated database for retrieving five types of mitochondrion-related information. The MitoTool is freely accessed at http:// www.mitotool.org.  ...  MitoTool, a web-based bioinformatics platform, is designed for deciphering human mitochondrial DNA (mtDNA) data in batch mode.  ...  advice on programming, to Deng-feng Zhang, Fu-hui Xiao and Yu Fan for helping with data input and to the other members of Yao's laboratory for helpful discussions.  ... 
doi:10.1016/j.mito.2010.09.013 pmid:20933105 fatcat:jpw5dtqktne5xn6plcgfu4pele

HmtDB, a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research

Marcella Attimonelli, Matteo Accetturo, Monica Santamaria, Daniela Lascaro, Gaetano Scioscia, Graziano Pappadà, Luigi Russo, Luigi Zanchetta, Mila Tommaseo-Ponzetta
2005 BMC Bioinformatics  
Intra-human and inter-species aminoacid variability data estimated on the 13 coding for proteins genes of the 1255 human genomes and 60 mammalian species are also available.  ...  HmtDB consists of a database of Human Mitochondrial Genomes, annotated with population data, and a set of bioinformatic tools, able to produce site-specific variability data and to automatically characterize  ...  The first step of both procedures is alignment of the human mitochondrial genomes.  ... 
doi:10.1186/1471-2105-6-s4-s4 pmid:16351753 pmcid:PMC1866381 fatcat:yihya56pwjgjdeijlqvaibt3rq

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  
bioinformatics tools dedicated to the mitochondrial genome.  ...  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  ...  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

MSeqDR: A Centralized Knowledge Repository and Bioinformatics Web Resource to Facilitate Genomic Investigations in Mitochondrial Disease

Lishuang Shen, Maria Angela Diroma, Michael Gonzalez, Daniel Navarro-Gomez, Jeremy Leipzig, Marie T. Lott, Mannis van Oven, Douglas C. Wallace, Colleen Clarke Muraresku, Zarazuela Zolkipli-Cunningham, Patrick F. Chinnery, Marcella Attimonelli (+3 others)
2016 Human Mutation  
MSeqDR is the Mitochondrial Disease Sequence Data Resource, a centralized and comprehensive genome and phenome bioinformatics resource built by the mitochondrial disease community to facilitate clinical  ...  PhenoTips is used for phenotypic data submission on de-identified patients using human phenotype ontology terminology.  ...  NWO) within the framework of the Forensic Genomics Consortium Netherlands (FGCN) to MvO.  ... 
doi:10.1002/humu.22974 pmid:26919060 pmcid:PMC4846568 fatcat:bzp3d5hrffb7hb4dupropvddka

V-MitoSNP: visualization of human mitochondrial SNPs

Li-Yeh Chuang, Cheng-Hong Yang, Yu-Huei Cheng, De-Leung Gu, Phei-Lang Chang, Ke-Hung Tsui, Hsueh-Wei Chang
2006 BMC Bioinformatics  
Mitochondrial single nucleotide polymorphisms (mtSNPs) constitute important data when trying to shed some light on human diseases and cancers.  ...  Visual input and output coupled with integrated mtSNP information from MITOMAP and NCBI make V-MitoSNP an ideal and complete visualization interface for human mtSNPs association studies.  ...  Acknowledgements This work is partly supported by the National Science Council in Taiwan under grant NSC94-2622-E-151-025-CC3, NSC94-2311-B037-001, NSC93-2213-E-214-037, NSC92-2213-E-214-036 and by the  ... 
doi:10.1186/1471-2105-7-379 pmid:16907992 pmcid:PMC1564046 fatcat:knrs67nnwvhcdkzlesfe66zb64

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).  ...  Further, we reassess the recent rediscovery of m.15287T4C by listing all known occurrences and, where possible, providing the haplogroup context, shedding new light on the potential pathogenicity status  ...  David Thorburn for useful information on an earlier case study. We also thank the anonymous reviewers for helpful comments on the early version of the manuscript.  ... 
doi:10.1002/humu.20846 pmid:18800376 fatcat:hthse4i4efb6jgge3h6fhe3acm

PON-mt-tRNA: a multifactorial probability-based method for classification of mitochondrial tRNA variations

Abhishek Niroula, Mauno Vihinen
2016 Nucleic Acids Research  
In the absence of evidence from segregation, biochemistry and histochemistry, PON-mt-tRNA classifies variations based on the machine learning method with an accuracy and MCC of 0.69 and 0.39, respectively  ...  We integrated a machine learning-based predictor and an evidence-based likelihood ratio for pathogenicity using evidence of segregation, biochemistry and histochemistry to predict the posterior probability  ...  ACKNOWLEDGEMENTS Faculty of Medicine, Lund University; Barncancerfonden; and Vetenskapsrådet. We thank Gerard Schaafsma for proofreading the manuscript.  ... 
doi:10.1093/nar/gkw046 pmid:26843426 pmcid:PMC4797295 fatcat:3pobxb56p5cglkapnidtcvumii

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

Hans-Jürgen Bandelt, Antonio Salas, Claudio M. Bravi
2006 Journal of Human Genetics  
By reanalyz ing some case studies of refractory anemia with ring sideroblasts, prostate cancer, and hearing impairment, we demonstrate that the practice of solely relying on MITOMAP can be most misleading  ...  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.  ...  It is most problematic when the potential pathogenic status of an observed mutation so strongly depends on the apparent novelty of the mutation, especially when the database search was incomplete.  ... 
doi:10.1007/s10038-006-0066-5 pmid:17021933 fatcat:b6osxsjgf5bwfny45qmsghaxny

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  ...  ACKNOWLEDGMENTS The authors are grateful for the contributions of Ying Liu, Saurav Sahay and Neha Narkhede during the development of this paper. The anonymous referees also provided useful comments.  ... 
doi:10.5626/jcse.2007.1.1.001 fatcat:sawebfga3bfybdibfq3yvhjf5u

High-confidence assessment of functional impact of human mitochondrial non-synonymous genome variations by APOGEE

Stefano Castellana, Caterina Fusilli, Gianluigi Mazzoccoli, Tommaso Biagini, Daniele Capocefalo, Massimo Carella, Angelo Luigi Vescovi, Tommaso Mazza, Yana Bromberg
2017 PLoS Computational Biology  
24,189 are all the possible non-synonymous amino acid changes potentially affecting the human mitochondrial DNA.  ...  mitochondrial non-synonymous genome variations.  ...  , as well as of databases of nuclear and mitochondrial precomputed predictions [9] [10] [11] [12] .  ... 
doi:10.1371/journal.pcbi.1005628 pmid:28640805 pmcid:PMC5501658 fatcat:t4pkw3zbfbgqre5zasfqjoil24

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

Resources, challenges and way forward in rare mitochondrial diseases research

Neeraj Kumar Rajput, Vipin Singh, Anshu Bhardwaj
2015 F1000Research  
This review focuses on the resources developed over the past years for analysis of genome data towards understanding disease biology especially in the context of mitochondrial diseases, given that mitochondria  ...  The review also describes crowdsourcing and crowdfunding efforts in rare diseases research and how the upcoming initiatives for understanding disease biology including analyses of large number of genomes  ...  MITOMAP Mitomap is a database of human mitochondrial genome. http://mitomap.org/MITOMAP 18.  ... 
doi:10.12688/f1000research.6208.2 pmid:26180633 pmcid:PMC4490798 fatcat:wvrbo4hhtreflnoffinuy6afhm
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