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Reports published and unpublished data on human mitochondrial DNA variation. MITOMASTER gives 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 sequences and single nucleotide variants may be analyzed. MITOMAP consists of three main sections: i) background information about the human mitochondrial DNA; ii) an annotated listing of mtDNA variants, both general population and patient; and iii) the MITOMASTER analysis tool.

mtDB / Human Mitochondrial Genome Database

A web-based database of human whole genome and complete coding region sequences. mtDB is the only comprehensive online source for the data contained within it. This includes the sequences themselves as many have not been deposited in a publicly available database such as GenBank. The list of mitochondrial polymorphisms continually grows with the addition of new sequences and is an important resource for phylogenetic and medical studies. The ability to search for multiple-variant haplotypes adds further detail to the latent data.

A free, web-accessible comprehensive list of breakpoints from three classes of somatic mtDNA rearrangements: circular deleted (deletions), circular partially duplicated (duplications) and linear mtDNAs. Currently, MitoBreak contains >1,400 mtDNA rearrangements from seven species (Homo sapiens, Mus musculus, Rattus norvegicus, Macaca mulatta, Drosophila melanogaster, Caenorhabditis elegans and Podospora anserina) and their associated phenotypic information collected from nearly 400 publications. The database allows researchers to perform multiple types of data analyses through user-friendly interfaces with full or partial datasets. It also permits the download of curated data and the submission of new mtDNA rearrangements. For each reported case, MitoBreak also documents the precise breakpoint positions, junction sequences, disease or associated symptoms and links to the related publications, providing a useful resource to study the causes and consequences of mtDNA structural alterations.

Mitodyn / MITOchondrial DYNamics

Allows users to add clinical phenotypes related to OPA1 variants. Mitodyn is a database specialized in genes involved in disorders affecting mitochondrial dynamics and bioenergetics. A query can be made by the database-ID, DNA change (cDNA), RNA protein, or reference. This database integrates data of the older eOPA1 website.

MitImpact / Mitochondrial mutation Impact

A collection of pre-computed pathogenicity predictions for all nucleotide changes that cause non-synonymous substitutions in human mitochondrial protein coding genes. MitImpact presents itself as a resource for fast and reliable evaluation of gene-specific susceptibility of unknown and verified amino acid changes.

Provides information about mitochondrial single nucleotide polymorphisms (SNPs). GiiB-JST mtSNP assists user in identification of mitochondrial single nucleotide polymorphisms (mtSNPs) associated with age-related conditions such as Alzheimer's disease, Parkinson's disease, or longevity. In overview, this online resource contains mitochondrial genome sequences related to individuals belonging to 7 different groups, where each group is composed of 96 individuals.

A database dedicated to the nuclear genes specifying the enzymes, structural proteins, and other proteins, many still not identified, involved in mitochondrial biogenesis and function.

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Big data scientist National institute of Plant Gneome Reseaech (NIPGR)

Research Interests Gene fusion detection in Plants Fusion transcripts (i.e., chimeric RNAs) resulting from gene fusions are well known in case of human. But, in plants, this phenomenon is not yet explored. We are planning to discover the fusion transcripts/gene fusions in different type of plants by using RNA-Seq datasets. Further, we are planning to understand the mechanism of gene fusion formation and significance of fusions in plants. Whole genome and transcriptome sequencing data analysis of Plants In this era of Next Generation Sequencing (NGS), there is huge amount of sequencing data available in the public domain. Any novel finding from these available datasets is major challenge for a computational biologist. We are interested in the analysis of whole genome and transcriptome sequencing data of different plants to fetch out the useful information from those datasets, with the help of bioinformatics tools. Currently, we are planning to study the gene clusters of secondary metabolite pathways in different plants. Development of webservers, databases and computational pipelines for plant research Development of database is necessary to compile and share the information with scientific community. We are dedicated to develop useful databases and webserver for plant research. Another area of interest is to develop automated pipelines and tools for the analysis of high throughput genomics data, generated by NGS technologies. Professional & Academic Background Staff Scientist II (May 2017- present): National Institute of Plant Genome Research (NIPGR), New Delhi, India Postdoctoral Research Associate (2015-2017): University Of Virginia, Charlottesville, VA, USA Research Scientist (2014-2015): Sir Ganga Ram Hospital, New Delhi, India PhD Bioinformatics (2009-2014): Bioinformatics Centre, Institute of Microbial Technology (IMTECH), Chandigarh under Jawaharlal Nehru University (JNU), New Delhi, India M.Sc. Life Sciences (2007-2009): Jawaharlal Nehru University (JNU), New Delhi, India B.Sc. Biotechnology (2004-2007): Jamia Millia Islamia (JMI), New Delhi, India Awards and Fellowships Junior and Senior Research Fellowship (2009-2014): Council of Scientific and Industrial Research (CSIR), New Delhi, India GATE (Graduate Aptitude Test in Engineering): Qualified in years 2008 and 2009 Scientific Contributions/ Recognitions Associate editor: Journal of Translational Medicine. Editorial Board Member of Journal: Theoretical Biology and Medical Modelling. Reviewer: PloS One, BMC Genomics, BMC Bioinformatics, BMC Biology, BMC Biotechnology, Frontiers in Physiology and several other journals. Web Resources/ Databases (Developed/ Contributed) A Platform for Designing Genome-Based Personalized Immunotherapy or Vaccine against Cancer (http://www.imtech.res.in/raghava/cancertope/) GenomeABC: A webserver for benchmarking of genome assemblers. (http://crdd.osdd.net/raghava/genomeabc/). Genomics web portal page. (http://crdd.osdd.net/raghava/genomesrs/). Map/Alignment module of CancerDr: Cancer Drug Resistance Database. (http://crdd.osdd.net/raghava/cancerdr/). Short reads and contigs alignment module of PCMDB: Pancreatic cancer methylation database. (http://crdd.osdd.net/raghava/pcmdb/). Burkholderia sp. SJ98 database. (http://crdd.osdd.net/raghava/genomesrs/burkholderia/). Rhodococcus imtechensis RKJ300 database. (http://crdd.osdd.net/raghava/genomesrs/rkj300/). Genotrick: A pipeline for whole genome assembly and annotation of Genomes (http://crdd.osdd.net/raghava/genomesrs/genotrick/) Development of Debian packages in OSDDlinux: A Customized Operating System for Drug Discovery. (http://osddlinux.osdd.net/). A Web-Based Platform for Designing Vaccines against Existing and Emerging Strains of Mycobacterium tuberculosis. (http://crdd.osdd.net/raghava/mtbveb/).

FusionFinder comrad

Mahantesh Biradar

‎Graduate PhD researcher focusing on Cardiovascular Epidemiology & Social Media Enthusiast Research Stash

I'm a Graduate PhD researcher in the area of Biomedical Science and focussing on the Pharmacogenomics/Pharmacogenomics of Diabetes and related complications

Science! SENS Research Foundation

MitoInteractome mtDB Multi-VORFFIP

Mitochondrial DNA variation databases | Genome annotation

Mutations in the human mitochondrial genome are known to cause an array of diverse disorders, most of which are maternally inherited, and all of which are associated with defects in oxidative energy metabolism. It is now emerging that somatic mutations in mitochondrial DNA (mtDNA) are also linked to other complex traits, including neurodegenerative diseases, ageing and cancer.

Source text:
(Schon et al., 2012) Human mitochondrial DNA: roles of inherited and somatic mutations. Nat Rev Genet.

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DNA sequence databases

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