To further simplify data analysis and polymorphism detection in the mitochondrial genome, we have created an annotated reference sequence which can be used in conjunction with several other sequence analysis programs developed at the University of Washington, Phred (Brent Ewing and Phil Green), Phrap (Phil Green), and Consed (David Gordon and Phil Green). This reference sequence contains polymorphism information downloaded from the MITOMAP database found at Emory University. In addition, we have developed a another program (Ref_Comp) which can parse output files created by the program Phrap, and automatically identify putative polymorphic sites in the mitochondrial genome (or any "reference" sequence).
For more information please refer to:
Rieder, M.J., Taylor, S.L., Tobe, V.O., and Nickerson, D.A., 1998, "Automating
the identification of DNA variations using quality-based fluorescence re-sequencing:
analysis of the human mitochondrial genome", Nucleic Acids Research, 26: