An Introduction to Mitochondrial Informatics

  • Hsueh-Wei Chang
  • Li-Yeh Chuang
  • Yu-Huei Cheng
  • De-Leung Gu
  • Hurng-Wern Huang
  • Cheng-Hong Yang
Part of the Methods in Molecular Biology book series (MIMB, volume 628)


In this chapter, we review the public resources available for human mitochondrial DNA and protein related bioinformatics, with a special focus on mitochondrial single nucleotide polymorphisms (mtSNPs). We also review our own freeware tool V-MitoSNP, giving an overview of its implementation and program workflow. Apart from these, we review several protocols for the graphic input of genes, keywords, gene searching by sequence, mtSNP searching by sequence, restriction enzyme mining, primer design, and virtual electrophoresis for PCR-RFLP genotyping. Some databases with similar function are integrated and compared.

Key words

Mitochondrial genome Variation Polymorphism SNP Database BLAST RFLP Genotyping Primer design 



This work was partly supported by the National Science Council in Taiwan under grant NSC97-2311-B-037-003-MY3, NSC96-2221-E-214-050-MY3, NSC96-2622-E214-004-CC3, and the grant KMU-EM-98-1.4.


  1. 1.
    Anderson, S., Bankier, A.T., Barrell, B.G., de Bruijn, M.H., Coulson, A.R., Drouin, J., et al. (1981) Sequence and organization of the human mitochondrial genome. Nature 290, 457–465.PubMedCrossRefGoogle Scholar
  2. 2.
    Andrews, R.M., Kubacka, I., Chinnery, P.F., Lightowlers, R.N., Turnbull, D.M., and Howell, N. (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23, 147.PubMedCrossRefGoogle Scholar
  3. 3.
    Taylor, R.W., and Turnbull, D.M. (2005) Mitochondrial DNA mutations in human disease. Nat Rev Genet 6, 389–402.PubMedCrossRefGoogle Scholar
  4. 4.
    Zanssen, S., and Schon, E.A. (2005) Mitochondrial DNA mutations in cancer. PLoS Med 2, e401.PubMedCrossRefGoogle Scholar
  5. 5.
    Pakendorf, B., and Stoneking, M. (2005) Mitochondrial DNA and human evolution. Annu Rev Genomics Hum Genet 6, 165–183.PubMedCrossRefGoogle Scholar
  6. 6.
    Ruiz-Pesini, E., Lott, M.T., Procaccio, V., Poole, J.C., Brandon, M.C., Mishmar, D., et al. (2007) An enhanced MITOMAP with a global mtDNA mutational phylogeny. Nucleic Acids Res 35, D823-D828.PubMedCrossRefGoogle Scholar
  7. 7.
    Ingman, M., and Gyllensten, U. (2006) mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. Nucleic Acids Res 34, D749-D751.PubMedCrossRefGoogle Scholar
  8. 8.
    Attimonelli, M., Accetturo, M., Santamaria, M., Lascaro, D., Scioscia, G., Pappada, G., et al. (2005) HmtDB, a human mitochondrial genomic resource based on variability studies supporting population genetics and biomedical research. BMC Bioinformatics 6 Suppl. 4, S4.PubMedCrossRefGoogle Scholar
  9. 9.
    O’Brien, E.A., Zhang, Y., Yang, L., Wang, E., Marie, V., Lang, B. F., and Burger, G. (2006) GOBASE - a database of organelle and bacterial genome information. Nucleic Acids Res 34, D697-D699.PubMedCrossRefGoogle Scholar
  10. 10.
    Chuang, L.Y., Yang, C.H., Cheng, Y.H., Gu, D.L., Chang, P.L., Tsui, K.H., and Chang, H.W. (2006) V-MitoSNP: visualization of human mitochondrial SNPs. BMC Bioinformatics 7, 379.PubMedCrossRefGoogle Scholar
  11. 11.
    Tanaka, M., Takeyasu, T., Fuku, N., Li-Jun, G., and Kurata, M. (2004) Mitochondrial genome single nucleotide polymorphisms and their phenotypes in the Japanese. Ann N Y Acad Sci 1011, 7–20.PubMedCrossRefGoogle Scholar
  12. 12.
    Johnson, M., Zaretskaya, I., Raytselis, Y., Merezhuk, Y., McGinnis, S., and Madden, T.L. (2008) NCBI BLAST: a better web interface. Nucleic Acids Res 36, W5-W9PubMedCrossRefGoogle Scholar
  13. 13.
    Packer, B.R., Yeager, M., Burdett, L., Welch, R., Beerman, M., Qi, L., et al. (2006) SNP500Cancer: a public resource for sequence validation, assay development, and frequency analysis for genetic variation in candidate genes. Nucleic Acids Res 34, D617-D621.PubMedCrossRefGoogle Scholar
  14. 14.
    Kent, W.J. (2002) BLAT - the BLAST-like alignment tool. Genome Res 12, 656–664.PubMedGoogle Scholar
  15. 15.
    Hinrichs, A.S., Karolchik, D., Baertsch, R., Barber, G.P., Bejerano, G., Clawson, H., et al. (2006) The UCSC Genome Browser Database: update 2006. Nucleic Acids Res 34, D590-D598.PubMedCrossRefGoogle Scholar
  16. 16.
    Behar, D.M., Rosset, S., Blue-Smith, J., Balanovsky, O., Tzur, S., Comas, D., et al. (2007) The Genographic Project public participation mitochondrial DNA database. PLoS Genet 3, e104.PubMedCrossRefGoogle Scholar
  17. 17.
    Brandstatter, A., Niederstatter, H., Pavlic, M., Grubwieser, P., and Parson, W. (2007) Generating population data for the EMPOP database - an overview of the mtDNA sequencing and data evaluation processes considering 273 Austrian control region sequences as example. Forensic Sci Int 166, 164–175.PubMedCrossRefGoogle Scholar
  18. 18.
    Ritchie, K., Myres, N.M., Angerhofer, N., Hughes, R., Ekins, J., Perego, U.A., and Woodward, S.R. (2008) The Sorenson Molecular Genealogy Foundation mtDNA Database. URL:
  19. 19.
    Attimonelli, M., Catalano, D., Gissi, C., Grillo, G., Licciulli, F., Liuni, S., Santamaria, M., Pesole, G., and Saccone, C. (2002) MitoNuc: a database of nuclear genes coding for mitochondrial proteins. Update 2002. Nucleic Acids Res 30, 172–173.PubMedCrossRefGoogle Scholar
  20. 20.
    Lemkin, P. F., Chipperfield, M., Merril, C., and Zullo, S. (1996) A World Wide Web (WWW) server database engine for an organelle database, MitoDat. Electrophoresis 17, 566–572.PubMedCrossRefGoogle Scholar
  21. 21.
    Prokisch, H., and Ahting, U. (2007) MitoP2, an integrated database for mitochondrial proteins. Methods Mol Biol 372, 573–586.PubMedCrossRefGoogle Scholar
  22. 22.
    Guda, P., Subramaniam, S., and Guda, C. (2007) Mitoproteome: human heart mitochondrial protein sequence database. Methods Mol Biol 357, 375–383.PubMedGoogle Scholar
  23. 23.
    Guda, C., Guda, P., Fahy, E., and Subramaniam, S. (2004) MITOPRED: a web server for the prediction of mitochondrial proteins. Nucleic Acids Res 32, W372-W374.PubMedCrossRefGoogle Scholar
  24. 24.
    Horton, P., Park, K.J., Obayashi, T., Fujita, N., Harada, H., Adams-Collier, C.J., and Nakai, K. (2007) WoLF PSORT: protein localization predictor. Nucleic Acids Res 35, W585-W587.PubMedCrossRefGoogle Scholar
  25. 25.
    Small, I., Peeters, N., Legeai, F., and Lurin, C. (2004) Predotar: a tool for rapidly screening proteomes for N-terminal targeting sequences. Proteomics 4, 1581–1590.PubMedCrossRefGoogle Scholar
  26. 26.
    Chen, H., Huang, N., and Sun, Z. (2006) SubLoc: a server/client suite for protein subcellular location based on SOAP. Bioinformatics 22, 376–377.PubMedCrossRefGoogle Scholar
  27. 27.
    Finn, R.D., Tate, J., Mistry, J., Coggill, P.C., Sammut, S.J., Hotz, H.R., et al. (2008) The Pfam protein families database. Nucleic Acids Res 36, D281-D288.PubMedCrossRefGoogle Scholar
  28. 28.
    Yu, X., Koczan, D., Sulonen, A.M., Akkad, D.A., Kroner, A., Comabella, M., et al. (2008) mtDNA nt13708A variant increases the risk of multiple sclerosis. PLoS One 3, e1530.PubMedCrossRefGoogle Scholar
  29. 29.
    Brandon, M.C., Lott, M.T., Nguyen, K.C., Spolim, S., Navathe, S.B., Baldi, P., and Wallace, D.C. (2005) MITOMAP: a human mitochondrial genome database - 2004 update. Nucleic Acids Res 33, D611-D613.PubMedCrossRefGoogle Scholar
  30. 30.
    Sherry, S.T., Ward, M.H., Kholodov, M., Baker, J., Phan, L., Smigielski, E.M., and Sirotkin, K. (2001) dbSNP: the NCBI database of genetic variation. Nucleic Acids Res 29, 308–311.PubMedCrossRefGoogle Scholar
  31. 31.
    Roberts, R.J., Vincze, T., Posfai, J., and Macelis, D. (2005) REBASE - restriction enzymes and DNA methyltransferases. Nucleic Acids Res 33 Database Issue, D230-D232.PubMedCrossRefGoogle Scholar
  32. 32.
    Chang, H.W., Yang, C.H., Chang, P.L., Cheng, Y.H., and Chuang, L.Y. (2006) SNP-RFLPing: restriction enzyme mining for SNPs in genomes. BMC Genomics 7, 30.PubMedCrossRefGoogle Scholar
  33. 33.
    Monson, K.L., Miller, K.W.P., Wilson, M.R., DiZinno, J.A., and Budowle, B. (2002) The mtDNA population database: an integrated software and database resource for forensic comparison. Forensic Sci Commun 4, AprilGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC 2010

Authors and Affiliations

  • Hsueh-Wei Chang
    • 1
  • Li-Yeh Chuang
    • 2
  • Yu-Huei Cheng
    • 2
  • De-Leung Gu
    • 2
  • Hurng-Wern Huang
    • 2
  • Cheng-Hong Yang
    • 2
  1. 1.Department of Biomedical Science and Environmental Biology, Center of Excellence for Environmental Medicine, Graduate Institute of Natural ProductsKaohsiung Medical UniversityKaohsiungTaiwan
  2. 2.Department of Biomedical Science and Environmental BiologyKaohsiung Medical UniversityKaohsiungTaiwan

Personalised recommendations