31,544 research outputs found

    SPRINT: Ultrafast protein-protein interaction prediction of the entire human interactome

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    Proteins perform their functions usually by interacting with other proteins. Predicting which proteins interact is a fundamental problem. Experimental methods are slow, expensive, and have a high rate of error. Many computational methods have been proposed among which sequence-based ones are very promising. However, so far no such method is able to predict effectively the entire human interactome: they require too much time or memory. We present SPRINT (Scoring PRotein INTeractions), a new sequence-based algorithm and tool for predicting protein-protein interactions. We comprehensively compare SPRINT with state-of-the-art programs on seven most reliable human PPI datasets and show that it is more accurate while running orders of magnitude faster and using very little memory. SPRINT is the only program that can predict the entire human interactome. Our goal is to transform the very challenging problem of predicting the entire human interactome into a routine task. The source code of SPRINT is freely available from github.com/lucian-ilie/SPRINT/ and the datasets and predicted PPIs from www.csd.uwo.ca/faculty/ilie/SPRINT/

    Efficient Antihydrogen Detection in Antimatter Physics by Deep Learning

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    Antihydrogen is at the forefront of antimatter research at the CERN Antiproton Decelerator. Experiments aiming to test the fundamental CPT symmetry and antigravity effects require the efficient detection of antihydrogen annihilation events, which is performed using highly granular tracking detectors installed around an antimatter trap. Improving the efficiency of the antihydrogen annihilation detection plays a central role in the final sensitivity of the experiments. We propose deep learning as a novel technique to analyze antihydrogen annihilation data, and compare its performance with a traditional track and vertex reconstruction method. We report that the deep learning approach yields significant improvement, tripling event coverage while simultaneously improving performance by over 5% in terms of Area Under Curve (AUC)

    Efficient seeding techniques for protein similarity search

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    We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets.We then perform an analysis of seeds built over those alphabet and compare them with the standard Blastp seeding method [2,3], as well as with the family of vector seeds proposed in [4]. While the formalism of subset seed is less expressive (but less costly to implement) than the accumulative principle used in Blastp and vector seeds, our seeds show a similar or even better performance than Blastp on Bernoulli models of proteins compatible with the common BLOSUM62 matrix

    Efficient seeding techniques for protein similarity search

    Get PDF
    We apply the concept of subset seeds proposed in [1] to similarity search in protein sequences. The main question studied is the design of efficient seed alphabets to construct seeds with optimal sensitivity/selectivity trade-offs. We propose several different design methods and use them to construct several alphabets.We then perform an analysis of seeds built over those alphabet and compare them with the standard Blastp seeding method [2,3], as well as with the family of vector seeds proposed in [4]. While the formalism of subset seed is less expressive (but less costly to implement) than the accumulative principle used in Blastp and vector seeds, our seeds show a similar or even better performance than Blastp on Bernoulli models of proteins compatible with the common BLOSUM62 matrix
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