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We present PEACE, a stand-alone tool for high-throughput ab initio clustering of transcript fragment sequences produced by Next Generation or Sanger Sequencing technologies. It is freely available from www.peace-tools.org. Installed and managed through a downloadable user-friendly graphical user interface (GUI), PEACE can process large data sets of(More)
The influenza A virus is a negative-stranded RNA virus composed of eight segmented RNA molecules, including polymerases (PB2, PB1, PA), hemagglutinin (HA), nucleoprotein (NP), neuraminidase (NA), matrix protein (MP), and nonstructure gene (NS). The influenza A viruses are notorious for rapid mutations, frequent reassortments, and possible recombinations.(More)
In this poster we describe the methods underlying EAST, a novel algorithm based on Minimum Spanning Trees for the de novo assembly of short-read, traditional, and hybrid transcript-derived fragments sets, resulting in a tool that: consistently outperforms several popular tools on longer sequences (e.g. Sanger sequencing data and longer 454 sequences); is(More)
  • Mufit Ozden
  • 2005
In this paper, a new metaheuristic optimization approach is developed for the mixed integer decisions with constraints within a simulation model. Each decision variable is handled by an optimizer that uses a machine learning technique. At the beginning of each iteration, the decisions are selected randomly from their decision distributions. The performance(More)
PEACE and EAST, together forming a pipeline for the clustering and assembly of EST transcript fragments, make use of a novel d<sup>2</sup>-based minimum spanning tree algorithm that results in quickly generated, high quality assemblies when applied to the results of Sanger sequencing. The tool is considerably more robust to sequencing error than competing(More)