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Hello! We are trying to compare our results with the currently available mutational spectra of mitochondrial DNA. For that purpose we would like to download the spectrum available on mitomap. However, on the web-tool it can only be queried 100bp at a time. Would it be possible to have the data for the whole mtDNA at once? and if so, How should we proceed? Best regards

Paulo Refinetti Per Ekstrom Christian Arstad

-- PerEkstrom - 08 Sep 2015


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Hello,

How do your results (generated by MitoMaster) and the results generated by Ancestry.com and Nat Geo differ? Of is that an impossible question to answer, given that the ability to manually choose the analysis parameters in MitoMaster?

Thanks

-- AndorJKiss - 14 Mar 2015


mtDNA Variants (includes mini insertions & deletions) and mtDNA mutations made it very difficult to use. We used to be able to see the list of all the variants on the same page and haplogroups, but now not able to do it anymore. We often nee to see multple variants on the same page, as well as the haplogroup distribution.

Is it possible to revert it to the previous version? Thank you.

Renkui Bai at GeneDx.

-- RenkuiBai - 11 Feb 2015


For information about the current set of GenBank sequences, please see http://www.mitomap.org/MITOMAP/GBFreqInfo

-- MarieLott - 18 Aug 2014


For a step-by-step walk-through of Mitomap & Mitomaster, see Lott, et al., mtDNA variation and analysis using MITOMAP and MITOMASTER, Current Protocols in Bioinformatics 44:1.23.1-1.23.26 (December 2013). http://onlinelibrary.wiley.com/doi/10.1002/0471250953.bi0123s44/full. If your library does not have a copy of this journal, a free PubMedCentral version of this article will become available in December 2014. You may also send an email to mitomap (at) email.chop.edu to request a PDF.

-- MarieLott - 18 Aug 2014


Point mutations and sequence IDs from the current GenBank set may be downloaded from http://www.mitomap.org/MITOMAP/Mitobank.

If you are a programmer and would like to download the entire database, please send an email to mitomap (at) email.chop.edu.

-- MarieLott - 18 Aug 2014


Is it possible that one can download the database?

-- JianyingLi - 29 May 2014


Hello,

Is it possible to download all Mitochondrial point mutations from your database?

Thanks, Thong

-- ThongNguyen - 27 May 2014


Dear Colleagues, You are cordially invited to join us for the 2013 NHLBI Mitochondrial Biology Symposium: Mitochondrial Genetics in Health and Disease. http://www.cvent.com/events/nhlbi-mitochondrial-biology-symposium-2013/event-summary-26f05e0e129748c8b816fafd1479f2de.aspx

The third in a series of biennial conferences focusing on mitochondrial biology, it will be held May 6–7, 2013, at the National Institutes of Health in Bethesda, Maryland. This symposium will build on the success of previous conferences and focus on the following: Genetics of Mitochondrial Diseases, Mitochondria and Aging and Mitochondria Genetics and Genomics. This symposium will bring together the leading thinkers in these areas of research to present the newest findings. We envision these presentations will spark debate and foster collaborations among participants with the goal of filling existing gaps in knowledge and advancing this fast-moving field.

Please visit meeting website: www.nhlbimitochondrialbiology.com for confirmed speakers and preliminary agenda. Additionally, the call for abstracts will open on Monday, December 17, 2012. We are seeking submissions from early career scientists, graduate students, or postdoctoral fellows in your department or program. Science awards and Oral Podium Presentation awards are available on a competitive basis. The Call for Abstracts will be open until March 29; please spread the word.

We hope you will be able to join us and look forward to welcoming you in Bethesda in May 2013 for the NHLBI Mitochondrial Biology Symposium: Mitochondrial Genetics in Health and Disease.

Thanks. Organizing Committee, NHLBI Mitochondria Biology Symposium

-- MarieLott - 11 Dec 2012


A new feature debuts on the SNP pages! We now have listed a variant's frequency in GenBank. This new GB frequency data is derived from 16,411 GenBank sequences with size greater than 14kbp. These sequences have been pre-loaded into Mitomaster and represent almost all haplogroups known to date. We will be updating and refining this set of sequences on a regular basis. As a caveat, please note that GenBank sequences may not be of equal quality (Yao, et al, 2009), that some of these sequences are from individuals with past, current or future disease, and that this portion of our data set has not been hand-curated by Mitomap.

-- MarieLott - 28 Nov 2012


A newly updated MITOMASTER tool set and the MITOMAP data set (with inclusion of Genbank variants) will finally be available very soon! We are hoping to have everything ready by December 2012. The latest "Beta" version of MITOMASTER is available now via the menu on the left.

-- MarieLott - 12 Nov 2012


Currentlly the MITOMASTER tools only work for human mtDNA. MarieLott - 12 Nov 2012

Since am working with mitochondrial regulated male sterility in chilli and onion, i would like to know how to process raw data of mtDNA sequence.

-- LakshmanaReddyDC - 26 Oct 2012


Hi Janet, we have changed it to A3307AA + T3308C. Thanks for bringing this to our attention MarieLott

There is a polymorphism listed on your site as T-TC at 3308, with a reference of Achilli 2008, pubMed 18335039. I believe this should be listed as T-AC: From the publication: "An extremely interesting case of a mutational motif marking a Native American branch of the mtDNA phylogeny is represented by the T3308A transversion with a subsequent insertion of one C (3308+C) that characterize haplogroup A2i." AACAACA TACCCATG CRS AACAACAACACCCATG From Genbank accession EU431080.2.

-- JanetCarr - 02 Nov 2011


Until MITOMASTER is up and running again, one can use HaploGrep (http://haplogrep.uibk.ac.at/) for the calculation of haplogroups from given polymorphsims - mtSNPs. It is based on the latest version of Phylotree (www.phylotree.org)

-- JohnnyWhitestone - 28 Sep 2011


Thank you for pointing this out, Richard. This has now been fixed. MarieLott

Re the table in http://www.mitomap.org/bin/view.pl/MITOMAP/MutationsRNA As I understand it, the entry for A1491G ("MT-RNR1 DEAF A1491G=A1555G 12S rRNA . . See 1555G references") should be omitted, since this, as mentioned in the original paper, refers to a position in E.coli 16s rRNA, NOT human mtDNA. Biochemical Evidence for Nuclear Gene Involvement in Phenotype of Non-Syndromic Deafness Associated with Mitochondrial 12S rRNA Mutation Min-Xin Guan, Nathan Fischel-Ghodsian andGiuseppe Attardi http://hmg.oxfordjournals.org/content/5/7/963.long

-- RichardThrift - 28 Sep 2011


We are considering adding the capability to select reference sequences in a future version of MITOMASTER. MarieLott

People with mtDNA data from 23andMe will be interested in medical implications of their data. There are thousands of 23andMe customers, and many will no doubt be curious. But 23andMe still uses the Yoruba reference, not CRS. Would it be possible to ADD a column to these pages: http://www.mitomap.org/bin/view.pl/MITOMAP/MutationsRNA http://www.mitomap.org/bin/view.pl/MITOMAP/MutationsCodingControl http://www.mitomap.org/bin/view.pl/MITOMAP/ClinicalPhenotypesRNA http://www.mitomap.org/bin/view.pl/MITOMAP/ClinicalPhenotypesPolypeptide http://www.mitomap.org/bin/view.pl/MITOMAP/MutationsLHON showing the Yoruba position, to make the tables usable directly by 23andMe customers?

Thanks Richard Thrift

-- RichardThrift - 25 Sep 2011


Marty is now working for Goddard contractor. Try contacting him via LinkedIn.

Does anyone have an email address for Marty Brandon? uci.edu is bouncing mbrandon@uci.edu

-- JohnElling - 14 Jul 2011


Thanks, Eric. We'll consider this. MarieLott

An allele search for 14674 shows m.14674T>C under both polymorphisms and confirmed mutations. The mutation report in Brain 2009, 132: 3165 should be cited. Listing this variant as a polymorphism is inviting misclassification in patient reporting.

Thanks, Eric Schmitt

-- EricSchmitt - 09 Jun 2011


This indeed was a typo and has now been fixed. Thanks MarieLott

I was wondering if the diagnostic SNP for J should be at location 13708 instead of 13078. I noticed this while using your table Diagnostic SNP table for my masters thesis. None of my sequences had a Guanine or Adenine at that (13078) location. However, location 13708 has many sequences with both Guanine and Adenine. This SNP also seems to correctly match the phylogenetic tree I generated.

Thanks, Melissa

-- MelissaRuda - 04 Nov 2010


MITOMASTER has now been rewritten & haplotyping is again available. Sorry that it took some time after the disruptive move from California to Philadelphia.

When will haplogroup function be restored to MitoMaster? Mark

-- MarquisVawter - 24 Sep 2010


It is an ever-evolving list, so no, it is not ALL of the nuclear genes (sorry).

Do the 2 lists of nuclear genes involved in mitochondrial disease (structural genes and non-structural genes at the bottom of the home page) include ALL genes involved in mitochondrial disease? If not, where can I find a complete list of all these genes?

Thank you,

Nathalie.

-- NathalieAbitbol - 14 Sep 2010


Using the SNV query tab in the updated MITOMASTER tools, you will get a report which lists haplotypes of sequences found with the variant in question. Hopefully this will be helpful. MarieLott
I would like to search all haplotypes for a specific change. Is this possible? we often pick up changes in our patients and never know if then are snp's or not. If where can I find all the possible haplotype changes listed together Thanks tricia

-- TriciaOwen - 25 Mar 2010


The Cytb locus you mentioned, 14748-15882, is for the Yoruba individual AF347015.1 . Mitomap uses the rCRS (NC_012920.1) as its standard, and for that the Cytb assignment is 14747-15887. MarieLott

It seems that the Cytb region is incorrectly assigned. In NCBI, the region includes 14748~15882. In this program, it refers 14747~15887.

-- MinShengPeng - 18 Jun 2009


Our updated MITOMASTER now assigns haplogroups per the latest Phylotree. If you continue to have problems, please send the sequence to us at the address at the top of the Feedback page. Thanks. MarieLott

I have a perfectly reasonable H haplogroup sequence that MITOMASTER insists on classifying as B2B. Other sequences a few bp different classify correctly

-- StevenMCarr - 18 Nov 2008


Done!

It will be a good idea to have capability of searching short mtDNA fragments (such as HV1 and HV2 regions) in Mitomaster. Thanks Dr. Amarjit Chahal chahala@molecularworldinc.com

-- AmarjitChahal - 20 Oct 2008


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