October 27, 2011 § Leave a Comment
As of October 26th 2011, a paper about the myKaryoView tool has been published in PLoS One. myKaryoView is a genome browser specifically designed for visualization of Direct-to-Consumer (DTC) personal genetic data. We look forward to receiving feedback from users visualizing their own personal genomes and developers willing to extend further the code or simply make use of myKaryoView in a different context.
The paper is freely available and open access.
Citation: Jimenez RC, Salazar GA, Gel B, Dopazo J, Mulder N, et al. (2011) myKaryoView: A Light-Weight Client for Visualization of Genomic Data. PLoS ONE 6(10): e26345. doi:10.1371/journal.pone.0026345
September 1, 2010 § Leave a Comment
Following my previous post on the First Publicly Available Genome Via DAS I would like to present an open source software that Rafael Jimenez and myself have developed for visualization of genomic data. Here we have it configured to display 23andMe data as a test case. We call it myKaryoView and it is available for free use and download. Its website is located at the following address:
myKaryoView works in most contemporary browsers without lengthy installations and uses publicly available data distributed throughout the Internet via DAS. This means that there is no need to hold the data locally and that it is capable of visualizing any data as long as it is available via DAS. In order to visualize 23andMe data, myKaryoView requires the set up of a DAS source, which currently limits myKaryoView’s usage to those familiar with this technology. However, configuration and addition of sources are extremely simple and the amount of data able to display is limited only to the time of request completion and data rendering.
Here we show myKaryoView to display personal genomics data with a dummy 23andMe genome data source. This source is based on real 23andMe results data from my own genome, randomly modified in a manner that is irrecognizably different.
The myKaryoView website shows an implementation that allows search of genome data via gene name or genome coordinates. For example, type in the search box 1:2000000,6000000 and hit “Submit Query”.
The figure above shows results of that query, with two tracks containing the source from 23andMe with dummy data plus genes for a subchromosomal region in chromosome 1, Start: 2000000, End: 60000000. Gene names and SNP data and are shown in red and blue respectively. Different color shades indicate the density of annotation for any given point. If the “Gene Names” data track name is clicked, a popup window appears with a link “Display Original Data Source” that allows the download of the raw data from its DAS source. Any feature can be clicked for retrieval of specific information contained in the DAS source. Here a blue SNP mark is clicked and a popup window appears describing the selected SNP and a link to its corresponding dbSNP entry.
A simple manual explaining how to install and configure myKaryoView to show different data sources is provided from the website. myKaryoView is still in beta testing and any feedback is welcome. We have some plans for the near future for myKaryoView, which we will reveal in due time. Meanwhile I hope you find it interesting and useful.
By the way, the claim that this is the First Open Source Visualization for 23andMe data is, of course, arguable.