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. 1998 Jan 1;26(1):120–125. doi: 10.1093/nar/26.1.120

Update of MmtDB: a Metazoa mitochondrial DNA variants database.

M Attimonelli 1, D Calò 1, A De Montalvo 1, C Lanave 1, D Sasanelli 1, M Tommaseo Ponzetta 1, C Saccone 1
PMCID: PMC147228  PMID: 9399815

Abstract

The present paper describes the improvements in MmtDB, a specialised database designed to collect Metazoa mitochondrial DNA variants. Priority in the data collection has been given to Metazoa for which a large amount of variants is available, e.g., for humans. Starting from the sequences available in the Nucleotide Sequence Databases, the redundant sequences have been removed and new sequences from other sources have been added. Value-added information is associated to each variant sequence, e.g., analysed region, experimental method, tissue and cell lines, population data, sex, age, family code and information about the variation events (nucleotide position, involved gene, restriction site gain or loss). Cross-references are introduced to the EMBL Data Library, as well as an internal cross-referencing among MmtDB entries according to tissual, heteroplasmic, familiar and aplotypical correlation. Furthermore MmtDB has a new section, AMmtDB: Aligned Metazoan mitochondrial biosequences. MmtDB can be accessed through the World Wide Web at URL http://WWW.ba.cnr.it/[symbol: see text]areamt08/MmtDBWWW.htm

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Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Anderson S., Bankier A. T., Barrell B. G., de Bruijn M. H., Coulson A. R., Drouin J., Eperon I. C., Nierlich D. P., Roe B. A., Sanger F. Sequence and organization of the human mitochondrial genome. Nature. 1981 Apr 9;290(5806):457–465. doi: 10.1038/290457a0. [DOI] [PubMed] [Google Scholar]
  2. Ayala F. J., Escalante A. A. The evolution of human populations: a molecular perspective. Mol Phylogenet Evol. 1996 Feb;5(1):188–201. doi: 10.1006/mpev.1996.0013. [DOI] [PubMed] [Google Scholar]
  3. Bairoch A., Boeckmann B. The SWISS-PROT protein sequence data bank. Nucleic Acids Res. 1991 Apr 25;19 (Suppl):2247–2249. doi: 10.1093/nar/19.suppl.2247. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Benson D., Lipman D. J., Ostell J. GenBank. Nucleic Acids Res. 1993 Jul 1;21(13):2963–2965. doi: 10.1093/nar/21.13.2963. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Cann R. L., Stoneking M., Wilson A. C. Mitochondrial DNA and human evolution. Nature. 1987 Jan 1;325(6099):31–36. doi: 10.1038/325031a0. [DOI] [PubMed] [Google Scholar]
  6. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  7. Devereux J., Haeberli P., Smithies O. A comprehensive set of sequence analysis programs for the VAX. Nucleic Acids Res. 1984 Jan 11;12(1 Pt 1):387–395. doi: 10.1093/nar/12.1part1.387. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Etzold T., Argos P. SRS--an indexing and retrieval tool for flat file data libraries. Comput Appl Biosci. 1993 Feb;9(1):49–57. doi: 10.1093/bioinformatics/9.1.49. [DOI] [PubMed] [Google Scholar]
  9. Giles R. E., Blanc H., Cann H. M., Wallace D. C. Maternal inheritance of human mitochondrial DNA. Proc Natl Acad Sci U S A. 1980 Nov;77(11):6715–6719. doi: 10.1073/pnas.77.11.6715. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Gouy M., Gautier C., Attimonelli M., Lanave C., di Paola G. ACNUC--a portable retrieval system for nucleic acid sequence databases: logical and physical designs and usage. Comput Appl Biosci. 1985 Sep;1(3):167–172. doi: 10.1093/bioinformatics/1.3.167. [DOI] [PubMed] [Google Scholar]
  11. Hauswirth W. W., Laipis P. J. Mitochondrial DNA polymorphism in a maternal lineage of Holstein cows. Proc Natl Acad Sci U S A. 1982 Aug;79(15):4686–4690. doi: 10.1073/pnas.79.15.4686. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Higgins D. G., Sharp P. M. Fast and sensitive multiple sequence alignments on a microcomputer. Comput Appl Biosci. 1989 Apr;5(2):151–153. doi: 10.1093/bioinformatics/5.2.151. [DOI] [PubMed] [Google Scholar]
  13. NASS M. M., NASS S. INTRAMITOCHONDRIAL FIBERS WITH DNA CHARACTERISTICS. I. FIXATION AND ELECTRON STAINING REACTIONS. J Cell Biol. 1963 Dec;19:593–611. doi: 10.1083/jcb.19.3.593. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Rice C. M., Fuchs R., Higgins D. G., Stoehr P. J., Cameron G. N. The EMBL data library. Nucleic Acids Res. 1993 Jul 1;21(13):2967–2971. doi: 10.1093/nar/21.13.2967. [DOI] [PMC free article] [PubMed] [Google Scholar]
  15. Saccone C. The evolution of mitochondrial DNA. Curr Opin Genet Dev. 1994 Dec;4(6):875–881. doi: 10.1016/0959-437x(94)90073-6. [DOI] [PubMed] [Google Scholar]
  16. Stoneking M., Jorde L. B., Bhatia K., Wilson A. C. Geographic variation in human mitochondrial DNA from Papua New Guinea. Genetics. 1990 Mar;124(3):717–733. doi: 10.1093/genetics/124.3.717. [DOI] [PMC free article] [PubMed] [Google Scholar]
  17. Torroni A., Wallace D. C. Mitochondrial DNA variation in human populations and implications for detection of mitochondrial DNA mutations of pathological significance. J Bioenerg Biomembr. 1994 Jun;26(3):261–271. doi: 10.1007/BF00763098. [DOI] [PubMed] [Google Scholar]
  18. Vigilant L., Stoneking M., Harpending H., Hawkes K., Wilson A. C. African populations and the evolution of human mitochondrial DNA. Science. 1991 Sep 27;253(5027):1503–1507. doi: 10.1126/science.1840702. [DOI] [PubMed] [Google Scholar]
  19. Wallace D. C. Diseases of the mitochondrial DNA. Annu Rev Biochem. 1992;61:1175–1212. doi: 10.1146/annurev.bi.61.070192.005523. [DOI] [PubMed] [Google Scholar]
  20. Wallace D. C. Mitochondrial genetics: a paradigm for aging and degenerative diseases? Science. 1992 May 1;256(5057):628–632. doi: 10.1126/science.1533953. [DOI] [PubMed] [Google Scholar]
  21. Ward R. H., Frazier B. L., Dew-Jager K., Päbo S. Extensive mitochondrial diversity within a single Amerindian tribe. Proc Natl Acad Sci U S A. 1991 Oct 1;88(19):8720–8724. doi: 10.1073/pnas.88.19.8720. [DOI] [PMC free article] [PubMed] [Google Scholar]
  22. Wolstenholme D. R. Animal mitochondrial DNA: structure and evolution. Int Rev Cytol. 1992;141:173–216. doi: 10.1016/s0074-7696(08)62066-5. [DOI] [PubMed] [Google Scholar]

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