Paolo Ribeca

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BACKGROUND The computation of the statistical properties of motif occurrences has an obviously relevant application: patterns that are significantly over- or under-represented in genomes or proteins are interesting candidates for biological roles. However, the problem is computationally hard; as a result, virtually all the existing motif finders use fast(More)
Approximate string matching is a very important problem in computational biology; it requires the fast computation of string distance as one of its essential components. Myers' bit-parallel algorithm improves the classical dynamic programming approach to Levenshtein distance computation, and offers competitive performance on CPUs. The main challenge when(More)
MOTIVATION Molecular chaperones prevent the aggregation of their substrate proteins and thereby ensure that they reach their functional native state. The bacterial GroEL/ES chaperonin system is understood in great detail on a structural, mechanistic and functional level; its interactors in Escherichia coli have been identified and characterized. However, a(More)
Next-generation sequencing technologies have opened up an unprecedented opportunity for microbiology by enabling the culture-independent genetic study of complex microbial communities, which were so far largely unknown. The analysis of metagenomic data is challenging: potentially, one is faced with a sample containing a mixture of many different bacterial(More)
—The FM-index is a data structure which is seeing more and more pervasive use, in particular in the field of high-throughput bioinformatics. Algorithms based on it show a pseudo-random memory access pattern. As a consequence, they are usually bound by memory bandwidth rather than CPU usage. Naive GPU implementations are no exception. Here we show that the(More)
The recent advent of high-throughput sequencing machines producing big amounts of short reads has boosted the interest in efficient string searching techniques. As of today, many mainstream sequence alignment software tools rely on a special data structure, called the FM-index, which allows for fast exact searches in large genomic references. However, such(More)
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