MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences

Department of Information and Computer Science, University of California, Irvine, Irvine, California 92697-3940, USA.
Human Mutation (Impact Factor: 5.14). 01/2009; 30(1):1-6. DOI: 10.1002/humu.20801
Source: PubMed


We have developed a computer system, MITOMASTER, to make analysis of human mitochondrial DNA (mtDNA) sequences efficient, accurate, and easily available. From imported sequences, the system identifies nucleotide variants, determines the haplogroup, rules out possible pseudogene contamination, identifies novel DNA sequence variants, and evaluates the potential biological significance of each variant. This system should be beneficial for mtDNA analyses of biomedical physicians and investigators, population biologists and forensic scientists. MITOMASTER can be accessed at

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Available from: Dan Mishmar, Oct 13, 2014
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    • "In the last years this gap progressively started to close with the release of a series of algorithms mainly focused on the haplogrouping process and, only in part, on the identification and annotation of the variability contained in the submitted samples. Successful examples in this field are MITOMASTER (Brandon et al., 2009), HaploGrep (Kloss-Brandstätter et al., 2011), HaploFind (Vianello et al., 2013) and HmtDB (Rubino et al., 2012). Nonetheless, these applications usually answer only to the first part of the problem: promising indentified mutations must then be analyzed to identify statistical significance with the phenotype under investigation. "
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    ABSTRACT: The last 30years of research greatly contributed to shed light on the role of mitochondrial DNA (mtDNA) variability in aging, although contrasting results have been reported, mainly due to bias regarding the population size and stratification, and to the use of analysis methods (haplogroup classification) that resulted to be not sufficiently adequate to grasp the complexity of the phenomenon. A 5-years European study (the GEHA EU project) collected and analysed data on mtDNA variability on an unprecedented number of long-living subjects (enriched for longevity genes) and a comparable number of controls (matched for gender and ethnicity) in Europe. This very large study allowed a reappraisal of the role of both the inherited and the somatic mtDNA variability in aging, as an association with longevity emerged only when mtDNA variants in OXPHOS complexes co-occurred. Moreover, the availability of data from both nuclear and mitochondrial genomes on a large number of subjects paves the way for an evaluation at a very large scale of the epistatic interactions at a higher level of complexity. This scenario is expected to be even more clarified in the next future with the use of next generation sequencing (NGS) techniques, which are becoming applicable to evaluate mtDNA variability and, then, new mathematical/bioinformatic analysis methods are urgently needed. Recent advances of association studies on age-related diseases and mtDNA variability will be also discussed in this review, taking into account the bias hidden by population stratification. Finally very recent findings in terms of mtDNA heteroplasmy (i.e. the coexistence of wild type and mutated copies of mtDNA) and aging as well as mitochondrial epigenetic mechanisms will be also discussed.
    Experimental gerontology 04/2014; 56. DOI:10.1016/j.exger.2014.03.022 · 3.49 Impact Factor
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    • "Summary of mitochondrial mutations in BE derived cell lines. Nucleotides for mutation locations and haplogroup designation based upon data from Mitomaster mitochondrial mutation database and analysis tool [26]. * indicates mutations that share their location with a known human mitochondrial polymorphism. "
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    ABSTRACT: Background Increased glycolysis is a hallmark of cancer metabolism, yet relatively little is known about this phenotype at premalignant stages of progression. Periodic ischemia occurs in the premalignant condition Barrett's esophagus (BE) due to tissue damage from chronic acid-bile reflux and may select for early adaptations to hypoxia, including upregulation of glycolysis. Methodology/Principal Findings We compared rates of glycolysis and oxidative phosphorylation in four cell lines derived from patients with BE (CP-A, CP-B, CP-C and CP-D) in response to metabolic inhibitors and changes in glucose concentration. We report that cell lines derived from patients with more advanced genetically unstable BE have up to two-fold higher glycolysis compared to a cell line derived from a patient with early genetically stable BE; however, all cell lines preserve active mitochondria. In response to the glycolytic inhibitor 2-deoxyglucose, the most glycolytic cell lines (CP-C and CP-D) had the greatest suppression of extra-cellular acidification, but were able to compensate with upregulation of oxidative phosphorylation. In addition, these cell lines showed the lowest compensatory increases in glycolysis in response to mitochondrial uncoupling by 2,4-dinitrophenol. Finally, these cell lines also upregulated their oxidative phosphorylation in response to glucose via the Crabtree effect, and demonstrate a greater range of modulation of oxygen consumption. Conclusions/Significance Our findings suggest that cells from premalignant Barrett's esophagus tissue may adapt to an ever-changing selective microenvironment through changes in energy metabolic pathways typically associated with cancer cells.
    PLoS ONE 02/2013; 8(2):e56884. DOI:10.1371/journal.pone.0056884 · 3.23 Impact Factor
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    • "by the data existing in its database. MITOMASTER (Brandon et al., 2009), a tool for the analysis of mtDNA sequences, resembles MitoTool essentially in data procedure. Nevertheless, it does not include the statistical function, the database query function and the missing variant inspection function. "
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    ABSTRACT: MitoTool, a web-based bioinformatics platform, is designed for deciphering human mitochondrial DNA (mtDNA) data in batch mode. The platform has advantages in (i) parsing diverse types of mtDNA data; (ii) automatically classifying haplogroup according to mtDNA sequences or variants; (iii) discovering possibly missing variants of the samples with claimed haplogroups status; (iv) estimating the evolutionary conservation index, protein coding effect and potential pathogenicity of certain substitutions; (v) performing statistical analysis for haplogroup distribution frequency between case and control groups. Furthermore, it offers an integrated database for retrieving five types of mitochondrion-related information. The MitoTool is freely accessed at
    Mitochondrion 10/2010; 11(2):351-6. DOI:10.1016/j.mito.2010.09.013 · 3.25 Impact Factor
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