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Filtration techniques in the form of rapid elimination of candidate sequences while retaining the true one are key ingredients of database searches in genomics. Although SEQUEST and Mascot perform a conceptually similar task to the tool BLAST, the key algorithmic idea of BLAST (filtration) was never implemented in these tools. As a result MS/MS protein(More)
Reliable identification of post-translational modifications is key to understanding various cellular regulatory processes. We describe a tool, InsPecT, to identify post-translational modifications using tandem mass spectrometry data. InsPecT constructs database filters that proved to be very successful in genomics searches. Given an MS/MS spectrum S and a(More)
Most tandem mass spectrometry (MS/MS) database search algorithms perform a restrictive search that takes into account only a few types of post-translational modifications (PTMs) and ignores all others. We describe an unrestrictive PTM search algorithm, MS-Alignment, that searches for all types of PTMs at once in a blind mode, that is, without knowing which(More)
Tandem mass spectrometry (MS/MS) experiments often generate redundant data sets containing multiple spectra of the same peptides. Clustering of MS/MS spectra takes advantage of this redundancy by identifying multiple spectra of the same peptide and replacing them with a single representative spectrum. Analyzing only representative spectra results in(More)
MOTIVATION Versatile and efficient variant calling tools are needed to analyze large scale sequencing datasets. In particular, identification of copy number changes remains a challenging task due to their complexity, susceptibility to sequencing biases, variation in coverage data and dependence on genome-wide sample properties, such as tumor polyploidy or(More)
BACKGROUND Adult granulosa cell tumors of the testis (AGCTT) are classified as sex cord-stromal tumors. Only 31 cases have been reported. Typical presentation includes a slowly enlarging, painless testicular mass. Associated findings are gynecomastia, decreased libido, and erectile dysfunction. Immunohistochemistry can be used to confirm the diagnosis. (More)
  • D J Hamer, T M Ward, S D Goldsworthy, Shaughnessy, Shaughnessy, Jason Reviewers +2 others
  • 2009
DISCLAIMER The authors warrant that they have taken all reasonable care in producing this report. The report has been through the SARDI Aquatic Sciences internal review process, and has been formally approved for release by the Editorial Board. Although all reasonable efforts have been made to ensure quality, SARDI Aquatic Sciences and Department for(More)
Motivation: Large-scale rearrangements and copy number changes combined with different modes of clonal evolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable variant calling tools and create well-calibrated benchmarks. Results: We developed a new simulation framework tHapMix that enables the creation of(More)
Motivation: Increased throughput and diverse experimental designs of large-scale sequencing studies necessitate versatile, scalable and robust variant calling tools. In particular, identification of copy number changes remains a challenging task due to their complexity, susceptibility to sequencing biases, variation in coverage data and dependence on(More)
MOTIVATION Large-scale rearrangements and copy number changes combined with different modes of clonal evolution create extensive somatic genome diversity, making it difficult to develop versatile and scalable variant calling tools and create well-calibrated benchmarks. RESULTS We developed a new simulation framework tHapMix that enables the creation of(More)
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