- mtDNA Tool:
- Variant Tool:
- Exome Prioritization
- Exome Priori. Target All
- Exome Priori. Result
- HBCR Exome
- Expert Panel
- Panel Tool:
- Panel Examiner
- PEDigree File
- 1 Mitochondrial Genomic Tools and Databases
- 1.1 MSeqDR is Collaborating with the Community to Bring Together Established Tools
- 1.2 Phenome Portal: Mitochondrial Diseases, Phenotypes, Tools and Databases
- 1.3 Mitochondrial DNA and nuclear DNA Variant Tools:
- 1.4 Mitochondrial DNA Tools:
- 1.5 GEM.APP at University of Miami
- 2 Other 3rd party mitochondrial tools and databases:
Mitochondrial Genomic Tools and Databases
MSeqDR is Collaborating with the Community to Bring Together Established Tools
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:
HBCR variant batch annotation, from a few variants to whole exomes
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
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.
Mitochondrial DNA Tools:
Phy-Mer , 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 , 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.
MITO Master at MITOMAP
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 MiamiExplore 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:
- MITOMAP, with ~10,300 expert annotated mitochondrial DNA variants, including ~580 with disease information.
A comprehensive on-line resource with curated datasets of mitochondrial DNA (mtDNA) rearrangements.
- HmtDB database
- PhyloTree phylogenetic tree of global human mitochondrial DNA variation
- POLG Database lists all known mutations in the coding region of the POLG gene.
- mtDB A resource for population genetics and medical sciences
- Mammalian Mitochondrial tRNA Genes
- mtDNA Manager
- HMPD – Human Mitochondrial Protein Database
A unique multi-national database holding clinical, biochemical and molecular genetic data
A comprehensive and reliable resource for massive extraction of sequences and sub-sequences of…
Provides comprehensive data on mitochondrial and human nuclear encoded proteins involved in…
A taxonomically broad organelle genome database that organizes and integrates diverse data…
An integrated web resource of mitochondrial proteomics for a wide range of organisms.
Focuses on the dynamic of mitochondrial protein formation through global mRNA analyses.
A database developed to assist the phylogeneticist user in retrieving individual gene sequence…
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.
- mvTool v.5: New report layout and new mtDNA variant data from 200,000 healthy people
- Recent publications from MSeqDR supported by the UMDF and NIH grants
- ClinGen / ClinVar – MSeqDR Working Groups & Expert Panels
- ClinGen approved the MSeqDR Consortium mitochondrial DNA Sequence Variant Interpretation (SVI) specifications
- U24 Mitochondrial Diseases Expert Panel is establishing 63 genes’ Leigh Disease associations at ClinGen
- MSeqDr joins FAIRsharing – A curated resource on data and metadata standards
- Quick-Mitome version 2 with new annotations, workflow, and tutorial
- Mondo Disease Ontology is coming to MSeqDR, Disease Portal received more disease entries
- MSeqDR to present tutorial workshop for the 5th year at the UMDF Mitochondrial Medicine Symposium
- mvTool v3: Added variant data from 40,000 people, Asians and Sadinians, meta-AF reference, new single variant report