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Provides a convenient, user-friendly interface for handling human mtDNA sequence data. It contains multiple modules which cover a wide array of functions: (i) to automatically yield a list of the variants in certain mtDNA relative to the revised Cambridge Reference Sequence (rCRS) recommended or the Reconstructed Sapiens Reference Sequence (RSRS) and determine the haplogroup status of that lineage according to Phylotree (www.phylotree.org), (ii) to detect missing sequence variants in certain mtDNA with claimed haplogroup status, (iii) to display the location of the variant, interspecies conservation index and change of amino acid status, (iv) to identify potentially pathogenic mutations based on the reported data, (v) to conduct statistical analysis for haplogroup distribution frequency between case and control groups, and (vi) to retrieve and batch download analytical output and mitochondrion-related data of interest.
A fast, automated process to determine distances between mtDNA sequences allowing their subsequent clustering and haplogroup assignment that may increase the speed of data analysis and avoid human errors. In order to avoid complexities/ambiguities resulting from recurrence and insertion/deletion phenomena and thus improving evolutionary signal-to-noise ratio, protein coding sequences were compared using a vectorial representation method, and the corresponding genetic distance matrix was used for the construction of a neighbor-joining/UPGMA tree or an MDS graphic, which generally agrees with the consensus mtDNA phylogeny.
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