Welcome to MitoAnalyzer



This program compares single nucleotide polymorphisms (SNPs) and mutations in human mitochondrial DNA (mtDNA) with the Cambridge Reference Sequence (Anderson et al., 1981). The numbering system is the same as that used by the Cambridge Reference Sequence. The program evaluates any single base pair changes, including polymorphisms, mutations, insertions, deletions, or substitutions in the sequence.


The program asks the user to answer the following questions:
  1. What type of change has occurred?

    • a single base pair insertion
    • a single base pair deletion
    • a single base pair substitution
  2. What is the number of the site of the change?


  3. If the change is an insertion, enter the number for the nucleotide immediately preceding the insertion.

    The next question only needs to be answered if the change is an insertion or substitution.
  4. What is the new nucleotide?

  5. Adenine, Cytosine, Guanine, or Thymine


The program provides the following information:


If the change is a substitution and occurs in a protein, then the following additional information prints out:
  1. the amino acid change resulting from the nucleotide change (e.g., tyrosine->asparagine)
  2. the position of the substituted base within the codon (1, 2, or 3)
  3. the position of the changed amino acid in the resultant protein (i.e., 14/500 indicates that the changed amino acid was the fourteenth codon in the string of 500 codons comprising the protein.)
  4. any mitochondrial disease associated with a mutation at the changed site that has been noted in the literature and come to the attention of the managers of this website.


If the change occurs in a protein, then the program allows the user to display all or a portion of the amino acid sequences of both the unchanged Cambridge Reference Sequence and the changed sequence.

The program will ask the following questions:
  1. Which portion of the protein do you wish to be displayed?
    1. "Whole sequence": The entire amino acid sequence of the protein affected by the change
    2. "1st affected-end": The amino acid sequence starting with the codon in which the changed site is located and ending at the end of the protein.
    3. "n before 1st affected-x after 1st affected": The amino acid sequence surrounding the codon in which the changed site is located. You will specify how large of a range around that codon you want to be displayed.
      Note: If the range that you indicate extends beyond the length of the protein, then the amino acid sequence will be displayed only until the end of the affected protein.
    4. "1st affected only": Only the codon in which the changed nucleotide is located
    5. "More information about the above options": Reminds you of what each of the above choices means. After reviewing, just select one of the choices.

    If you choose option a, b, or c from above, then the program will ask the following question:
  2. How should the amino acids be abbreviated when printing the amino acid sequence?
    • One-letter abbreviations (e.g., P, S, F, W)
    • Three-letter abbreviations (e.g., pro, ser, phe, trp)
    • Full names (e.g., proline, serine, phenylalanine, tryptophan)
    Note: use one-letter abbreviations for very long sequences; for example, if you choose "whole sequence" or "1st affected-end"
  3. If you choose option c from question 1 above, you will be instructed to specify how many amino acids before the codon in which the changed site is located should be printed by entering the number of amino acids into the textfield labeled "Sequence Range" and pressing enter. Then, you will be instructed to specify how many amino acids following the codon in which the changed site is located should be printed by entering the number of amino acids into the same textfield and pressing enter.


If an error occurs, a message will be printed to the screen in red.
Errors can occur for the following reasons:

If you encounter an error, simply enter the correct value in the appropriate location.

If you want to run the program again, simply change any of the values in the user interface. You will have to re-answer all questions following that point.





REFERENCES

Anderson, S., Bankier, A.T., Barrell, B.G., deBrujin, M.H.L., Coulson, A.R., Drouin, J., Eperon, I.C., Nierlich, D.P., Roe, B.A., Sanger, F., Schreier, P.H., Smith, A.J.H., Staden, R., Young, I.G. 1981. Sequence and Organization of the Human Mitochondrial Genome. Nature 290, 457-465.

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