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. 2013 Dec;44(123):1.23.1-26.
doi: 10.1002/0471250953.bi0123s44.

mtDNA Variation and Analysis Using Mitomap and Mitomaster

Marie T Lott  1 , Jeremy N Leipzig  2 , Olga Derbeneva  3 , H Michael Xie  4 , Dimitra Chalkia  5 , Mahdi Sarmady  6 , Vincent Procaccio  7 , Douglas C Wallace  8
Affiliations

mtDNA Variation and Analysis Using Mitomap and Mitomaster

Marie T Lott et al. Curr Protoc Bioinformatics. 2013 Dec.

Abstract

The Mitomap database of human mitochondrial DNA (mtDNA) information has been an important compilation of mtDNA variation for researchers, clinicians and genetic counselors for the past twenty-five years. The Mitomap protocol shows how users may look up human mitochondrial gene loci, search for public mitochondrial sequences, and browse or search for reported general population nucleotide variants as well as those reported in clinical disease. Within Mitomap is the powerful sequence analysis tool for human mitochondrial DNA, Mitomaster. The Mitomaster protocol gives step-by-step 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 identifiers and single nucleotide variants may be analyzed.

Keywords: GenBank sequences; biological database; haplogroups; human mitochondrial DNA; information retrieval; single nucleotide variants; species conservation.

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Figures

Figure 1
Figure 1. The home page of www.mitomap.org
Figure 2
Figure 2. Essential mtDNA Background Information
Figure 3
Figure 3. The rCRS
Figure 4
Figure 4. Complete Mitochondrial DNA Sequences
Figure 5
Figure 5. The mitochondrial genetic code
Figure 6
Figure 6. Haplogroup Frequency Estimates
Figure 7
Figure 7. Diagnostic RFLP and SNPs for Major Haplogroups
Figure 8
Figure 8. mtDNA Haplogroup Migration Map
Figure 9
Figure 9. Simplified Mitochondrial Haplogroup Relationships
Figure 10
Figure 10. Mitochondrial Functional Locations
Figure 11
Figure 11. Gene map of the human mitochondrial DNA with representative disease variants shown
Figure 12a
Figure 12a
Search box for specific variant(s).
Figure 12b
Figure 12b
Search box for specific variant(s). In this example, a single position is queried.
Figure 12c
Figure 12c
Results for variant search. In this example, a range was queried. This screenshot shows only a portion of the results returned.
Figure 13
Figure 13
Links to MITOMAP Variants. Variants are organized into two categories – general variants (top section) and those with reports of possible disease-associations (lower section).
Figure 14a
Figure 14a
Control Region Variants.
Figure 14b
Figure 14b
Outside of the Control Region: Coding and RNA Variants.
Figure 15
Figure 15
Variant information can be sorted.
Figure 16
Figure 16. Details of GB set frequency
Figure 17
Figure 17. GenBank ID links to sequence
Figure 18
Figure 18. Pub Med ID links to publication
Figure 19
Figure 19. Predicted Haplogroup links to total listing of sequences with that haplogroup in the GenBank sequence set
Figure 20
Figure 20. MITOMASTER analysis report on each sequence
Figure 21
Figure 21. Reported Coding and Control Region mutations found in patients
Figure 22
Figure 22. Reported rRNA and tRNA mutations found in patients
Figure 23
Figure 23. Sample Sequence EU915478 at GenBank
Figure 24
Figure 24. Send FASTA dialog box
Figure 25
Figure 25. Submit Sequence screen
Figure 26
Figure 26. Alignment Summary
Figure 27
Figure 27. rCRS Track View
Figure 28
Figure 28. Sequence Alignment, areas of interest circled
Figure 29
Figure 29. Alignment Detail
Figure 30
Figure 30. Alignment Details, areas of interest circled
Figure 31A
Figure 31A. Conservation Grid
Figure 31B
Figure 31B. Conservation Grid of Species
Figure 32
Figure 32. Submitting GenBank Identifiers
Figure 33
Figure 33. Single Nucleotide Variant Submission
See this image and copyright information in PMC

References

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