MitoWheel, visualizing the human mitochondrial genome

Abstract

AbstractSo far researchers, web users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA and find a region of interest. But with MitoWheel the situation is about to change. MitoWheel is a graphical representation of the circular human mitochondrial genome available on the web at "http://mitowheel.org":http://mitowheel.org.The human mitochondrial DNA is a 16569 basepair long, circular molecule and this very circularity is the basic idea behind MitoWheel. The mitochondrial genome can be represented with a wheel and by spinning this wheel users can quickly scan through, browse and identify the particular regions. The spinning is via click-and-drag or by using the left and right arrows in the sequence bar.The sequence used is the standard Revised Cambridge Reference Sequence. The main components of the application are a search box, a sequence bar and the wheel itself.The most important feature of the MitoWheel is its versatile search function. As an output of a query the wheel and the sequence bar stops at the searched nucleotide position or sequence and additional information (whether the nucleotide or the sequence is part of a gene or other specific region) can be seen on a pop-up window. People can search for a nucleotide position or sequence in the search box with numbers (15450, 8366-8572), with nucleotides (ATGCTAAAA), search for an encoded gene or specific region by abbreviations (atp8), genes (complex III, cytochrome b) and sequence features, even mutations (12276A) with the possible functional effects of the mutation. Selected sequences or their reverse complementary sequences can be send to the clipboard and saved.MitoWheel incorporates data on fully sequenced human mitochondrial genomes that have been deposited in the GenBank nucleotide database by different research groups. The sequence bar contains information not only about the function of specific nucleotides, but also about allele frequencies at polymorphic positions.MitoWheel was developed by human mitochondrial geneticist Gábor Zsurka, the wheel was made with Flash Professional 8.0 and the code harnessed the power of Actionscript, a scripting language designed specially for Flash. Attila Csordás is the other member of the developer group. The web application can be useful for anybody interested in human mitochondrial genetics and its biological, medical consequences.