Mitochondrial Genomic Tools and Databases

MSeqDR is Collaborating with the Community to Bring Together Established Tools

Phenome Portal: Mitochondrial Diseases, Phenotypes, Tools and Databases

Disease Portal: All MSeqDR data linked to the disease in a single place

Select a Mitochondrial Disease from the list and view the integrated annotations for associated symptoms, genes, and variants. Data represents in-house effort in compiling disease data from ClinVar, CTDBase, OMIM, HPO, UMDF, NAMDC.

HPO Browser: Browse and traversing human phenotype ontology tree

View a terms's parent, sister and child terms, along with potential matching diseases. Compare with HPO's report: (HP:0000118)

Mitochondrial DNA and nuclear DNA Variant Tools:

mvTool - Universal mtDNA variant converter and one stop annotation:

mvTool converts dozens of mtDNA variant formats into a standard rCRS-based HGVS format. It also converts YRI-based positions into rCRS-based positions. Plus mtDNA specific one-stop variant annotations, with multiple-population frequencies from major mtDNA resources from Mitomap, HmtDB, and the community.

VariantOneStop: Complete genomic annotations plus multiple-population frequencies, variant name checking and conversion

It combines MSeqDR's own data, Ensembl VEP, Mutalyzer, ClinVar, multiple sources including PolyPhen, SIFT, the dbNSFP resource, and the CADD scores.

It is also the back-end engine for our variant submission tool.

HBCR (retiring) variant batch annotation, from a few variants to whole exomes  Help file 

The Human BP Codon Resource Variant Annotation Pipeline (HBCR) tool is developed by Dr. Xiaowu Gai.

The HBCR is a perl and MySQL program that functionally annotates variants. Predicted sequence changes are based on Ensembel gene models, and pathogenicity data is extracted from our curated database, and multiple sources including PolyPhen, SIFT, the dbNSFP resource, and the CADD: Combined Annotation Dependent Depletion scores. It supports input in HGVS, VCF (v.4 or above), or HBCR text formats. This tools is retiring and largely replaced with VariantOneStop. It is kept mainly for back-compatibility.

Mitochondrial DNA Tools:

Phy-Mer Help file, web service for MSeqDR's own haplogroup classifier tool.

Phy-Mer is a novel alignment-free and reference-independent tool, and it supports input in fasta, fastq, bam, csv formats Pubmed 25505086.

MToolBox Help file, A pipeline for human mtDNA analysis from sequencing data.

MToolBox software implements an effective computational strategy for human mitochondrial genomes assembling and analysis from mitochondria-targeted and off-targeted sequencing data. The summary of the analysis include: reconstructed mitochondrial genomes (for NGS data), haplogroup(s) prediction, and functional annotation of prioritized variants.


MITOMAP: A human mitochondrial genome database, featuring manually curated polymorphisms and mutations. Lead by Dr. Doug Wallace, curated by Marie Lott. The MITOMAP database and MITOMASTER tools are being upgraded by Jeremy N Leipzig and Michael Xie of the CHOP.


A Project lead by Dr. Marcella Attimonelli. HmtDB is a Human Mitochondrial Genomic Resource Based on Variability Studies Supporting Population Genetics and Biomedical Research.


MT.AT: Dr. Fons Stassen.

GEM.APP at University of Miami

Explore genomic variant data from patients and families with defined diseases. The site is open to the public for a gene-by-gene search and can be filtered by phenotypes and inheritance patterns. Users usually have a distinct hypothesis for a specific gene, such as identifying rare variants that are supportive of disease association.

Other 3rd party mitochondrial tools and databases:


General tools and databases:

Genome Build Conversion Tools

1.  The NCBI Genome Remapping Service is a great option to remap between assembly versions.  This offers conversion to/from GRCh38. It also offeres "Clinical Remap" and "Alt Remap".

2.  The UCSC conversion tool allows you to convert genome coordinates and genome annotation files between assemblies.  This offers conversion to/from GRCh38. It includes the major GRC builds as well as the earlier NCBI versions.  The current version supports both forward and reverse conversions, as well as conversions between selected species.

3.  The Ensembl Assembly Converter - Allows conversion of NCBI 36 and GRCh37 to GRCh38.