Browsing by Subject "Genome annotation"

Now showing 1 - 1 of 1
  • Thumbnail Image
    Item
    SpectroGene: A Tool for Proteogenomic Annotations Using Top-Down Spectra
    (ACS Publications, 2016-01-04) Kolmogorov, Mikhail; Liu, Xiaowen; Pevzner, Pavel A.; BioHealth Informatics, School of Informatics and Computing
    In the past decade, proteogenomics has emerged as a valuable technique that contributes to the state-of-the-art in genome annotation; however, previous proteogenomic studies were limited to bottom-up mass spectrometry and did not take advantage of top-down approaches. We show that top-down proteogenomics allows one to address the problems that remained beyond the reach of traditional bottom-up proteogenomics. In particular, we show that top-down proteogenomics leads to the discovery of previously unannotated genes even in extensively studied bacterial genomes and present SpectroGene, a software tool for genome annotation using top-down tandem mass spectra. We further show that top-down proteogenomics searches (against the six-frame translation of a genome) identify nearly all proteoforms found in traditional top-down proteomics searches (against the annotated proteome). SpectroGene is freely available at http://github.com/fenderglass/SpectroGene .