The file Mito_Ref_Variants.phd.1 is a ".phd" which is compatible with the three sequencing analysis software programs created at the University of Washington. This suite of programs consists of Phred (base-calling), Phrap (contig assembly), and Consed (sequence/contig viewing). This mitochondrial reference sequence (the Anderson or Cambridge sequence) has the same format as files generated by the program Phred (i.e. all files with a .phd extension) and can be used by Phrap during contig assembly, and viewed using Consed. When viewed with Consed the sequence will contain "tags" which highlight specific bases which have been reported in the scientific literature as having a polymorphism at that site. All annotation contained within these tags was uploaded from the MITOMAP database at Emory Univesity. By reformatting this data to be used within the Phred/Phrap/Consed environment, this .phd file provides a "visual" database of all known mitochondrial polymorphisms and simplifies data analysis within the Consed environment.
Usage notes: The programs Phred/Phrap/Consed require a specific directory structure. If you are not familiar with these programs you can check them out at www.genome.washington.edu. In brief, you must have three subdirectories, these include:
In order to be included in an assembly by the program Phrap, all .phd files must be in ./phd_dir. In order to include the mitochondrial reference sequence in your assembly, copy Mito_Ref_Variants.phd.1 into the ./phd_dir subdirectory. After assemblying your sequence files with Phrap, any sequence generated from a mitochondrial DNA template should be included in the same contig along with your reference sequence.
When working in Consed, you can view the contig which contains the file Mito_Ref_Variants.phd.1 along with all of the other mitochondrial sequence which assembled with the reference sequence. By using mouse button 3, and clicking on any of the highlighted bases, a window will appear which gives all of the information for that site of the mitochondrial genome.