We are grateful to our colleagues for their great contributions in providing the original sequence data, reference information and ideas for modules. The database section contains compiled information from MITOMAP, mtDB, MitoCarta, Mamit-tRNA, MitoRes, PhyloTree and NCBI.
Links of useful databases:
PhyloTree
MITOMAP
mtDB
HmtDB
MitoCarta
mtSNP
MitoVariome
MitoRes
MitoProteome
Mamit-tRNA
POLG
Links of useful tools:
MITOMASTER
MitoWheel
MitoAnalyzer
mtDNAmanager
MtSNPscore
eCOMPAGT
V-MitoSNP
HaploGrep 2
References
1. Anderson S, Bankier AT, Barrell BG, de Bruijn MH, Coulson AR, Drouin J, Eperon IC, Nierlich DP, Roe BA, Sanger F, et al: Sequence and organization of the human mitochondrial genome. Nature 1981, 290:457-465.
2. Torroni A, Achilli A, Macaulay V, Richards M, Bandelt H-J: Harvesting the fruit of the human mtDNA tree. Trends Genet 2006, 22:339-345.
3. Salas A, Bandelt H-J, Macaulay V, Richards MB: Phylogeographic investigations: the role of trees in forensic genetics. Forensic Sci Int 2007, 168:1-13.
4. Tanaka M, Cabrera VM, Gonzalez AM, Larruga JM, Takeyasu T, Fuku N, Guo LJ, Hirose R, Fujita Y, Kurata M, et al: Mitochondrial genome variation in eastern Asia and the peopling of Japan. Genome Res 2004, 14:1832-1850.
5. Attimonelli M, Accetturo M, Santamaria M, Lascaro D, Scioscia G, Pappada G, Russo L, Zanchetta L, Tommaseo-Ponzetta M: HmtDB, a human mitochondrial genomic resource based on variability studies supporting population genetics and biomedical research. BMC Bioinformatics 2005, 6 Suppl 4:S4.
6. Brandon MC, Lott MT, Nguyen KC, Spolim S, Navathe SB, Baldi P, Wallace DC: MITOMAP: a human mitochondrial genome database--2004 update. Nucleic Acids Res 2005, 33:D611-613.
7. Ingman M, Gyllensten U: mtDB: Human Mitochondrial Genome Database, a resource for population genetics and medical sciences. Nucleic Acids Res 2006, 34:D749-751.
8. Lee YS, Kim W-Y, Ji M, Kim JH, Bhak J: MitoVariome: a variome database of human mitochondrial DNA. BMC Genomics 2009, 10 Suppl 3:S12.
9. Catalano D, Licciulli F, Turi A, Grillo G, Saccone C, D'Elia D: MitoRes: a resource of nuclear-encoded mitochondrial genes and their products in Metazoa. BMC Bioinformatics 2006, 7:36.
10. Cotter D, Guda P, Fahy E, Subramaniam S: MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res 2004, 32:D463-467.
11. Putz J, Dupuis B, Sissler M, Florentz C: Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures. RNA 2007, 13:1184-1190.
12. Bhardwaj A, Mukerji M, Sharma S, Paul J, Gokhale CS, Srivastava AK, Tiwari S: MtSNPscore: a combined evidence approach for assessing cumulative impact of mitochondrial variations in disease. BMC Bioinformatics 2009, 10 Suppl 8:S7.
13. Zsurka G, Csordás A: MitoWheel, visualizing the human mitochondrial genome Nature Precedings 2009, [http://dx.doi.org/10.1038/npre.2009.3167.1].
14. Lee MS, Levin BC: MitoAnalyzer, a computer program and interactive web site to determine the effects of single nucleotide polymorphisms and mutations in human mitochondrial DNA. Mitochondrion 2002, 1:321-326.
15. Lee HY, Song I, Ha E, Cho S-B, Yang WI, Shin K-J: mtDNAmanager: a Web-based tool for the management and quality analysis of mitochondrial DNA control-region sequences. BMC Bioinformatics 2008, 9:483.
16. Brandon MC, Ruiz-Pesini E, Mishmar D, Procaccio V, Lott MT, Nguyen KC, Spolim S, Patil U, Baldi P, Wallace DC: MITOMASTER: a bioinformatics tool for the analysis of mitochondrial DNA sequences. Hum Mutat 2009, 30:1-6.
17. Weissensteiner H, Schonherr S, Specht G, Kronenberg F, Brandstatter A: eCOMPAGT integrates mtDNA: import, validation and export of mitochondrial DNA profiles for population genetics, tumour dynamics and genotype-phenotype association studies. BMC Bioinformatics 2010, 11:122.
18. Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N: Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 1999, 23:147.
19. BioPerl project. [http://www.bioperl.org/].
20. Comprehensive Perl Archive Network (CPAN). [http://www.cpan.org/].
21. Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, Valentin F, Wallace IM, Wilm A, Lopez R, et al: Clustal W and Clustal X version 2.0. Bioinformatics 2007, 23:2947-2948.
22. van Oven M, Kayser M: Updated comprehensive phylogenetic tree of global human mitochondrial DNA variation. Hum Mutat 2009, 30:E386-394.
23. Ruiz-Pesini E, Mishmar D, Brandon M, Procaccio V, Wallace DC: Effects of purifying and adaptive selection on regional variation in human mtDNA. Science 2004, 303:223-226.
24. The R Project for Statistical Computing. [http://www.r-project.org/].
25. Chuang L-Y, Yang C-H, Cheng Y-H, Gu D-L, Chang P-L, Tsui K-H, Chang H-W: V-MitoSNP: visualization of human mitochondrial SNPs. BMC Bioinformatics 2006, 7:379.
26. Bandelt H-J, Lahermo P, Richards M, Macaulay V: Detecting errors in mtDNA data by phylogenetic analysis. Int J Legal Med 2001, 115:64-69.
27. Yao Y-G, Bravi CM, Bandelt H-J: A call for mtDNA data quality control in forensic science. Forensic Sci Int 2004, 141:1-6.
28. Yao Y-G, Salas A, Logan I, Bandelt H-J: mtDNA data mining in GenBank needs surveying. Am J Hum Genet 2009, 85:929-933.
29. Carracedo A, Bar W, Lincoln P, Mayr W, Morling N, Olaisen B, Schneider P, Budowle B, Brinkmann B, Gill P, et al: DNA commission of the international society for forensic genetics: guidelines for mitochondrial DNA typing. Forensic Sci Int 2000, 110:79-85.
30. Pagliarini DJ, Calvo SE, Chang B, Sheth SA, Vafai SB, Ong S-E, Walford GA, Sugiana C, Boneh A, Chen WK, et al: A mitochondrial protein compendium elucidates complex I disease biology. Cell 2008, 134:112-123.