From sequences of the mtDNA control region (500 bp) we identified 28 unique haplotypes from 30 variable sites. For 2193 biopsy samples collected from whales in 10 feeding regions and 8 breeding regions dur-ing the winter and summer of 2004 to 2006, we first used microsatellite genotyping (average, 9.5 loci) to identify replicate samples. We quantified the relative influence of maternal fidelity to feeding grounds and natal fidelity to breeding grounds on the population structure of humpback whales Megaptera novae -angliae based on an ocean-wide survey of mitochondrial (mt) DNA diversity in the North Pacific. PHFinder is flexible, enabling explicit specification of key parameters to infer double peaks (i.e., heteroplasmies). PHFinder detected most (90%) of the known heteroplasmies thereby greatly reducing the amount of visual inspection required. The program was tested with Sanger sequencing data from 100 humpback whale ( Megaptera novaeangliae ) tissue samples with known heteroplasmies. PHFinder automatically identifies point heteroplasmies directly from the chromatogram trace data. Here, we present PHFinder, a Python-based, open source tool to assist in the detection of point heteroplasmies in large numbers of Sanger chromatograms.
SNAPGENE TRACE SOFTWARE
Few software solutions are available to automate the detection of point heteroplasmies, and those that are available are typically proprietary, lack customization or are unsuitable for automated heteroplasmy assessment in large datasets. Visual inspection of chromatograms is both consuming and highly subjective, as heteroplasmy is difficult to differentiate from background noise. Heteroplasmy can be detected by visual inspection of Sanger sequencing chromatograms, where it appears as multiple peaks of fluorescence at a single nucleotide position. Heteroplasmy is the presence of two or more organellar genomes (mitochondrial or plastid DNA) in an organism, tissue, cell or organelle.
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