The sequence analysis tools found here were developed as part of a project to sequence the entire mitochondrial genome in a single pass and perform rapid detection of polymorphisms (differences from the Anderson (Cambridge) reference sequence). To select primers to amplify long tracts of DNA, such as mtDNA, in overlapping segments, we have created a program known as PCR-Overlap that works together with the primer picking program, Primer3, available at the Whitehead Institute.  PCR-Overlap automates the selection of primer sets based on the product size and product overlap defined by the user for the reference sequence of interest, e.g. mitochondrial genome.

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:  967-973.