Error correction method for sequencing data with insertions and deletions
نویسندگان
چکیده
منابع مشابه
MapReduce for accurate error correction of next-generation sequencing data
Motivation Next-generation sequencing platforms have produced huge amounts of sequence data. This is revolutionizing every aspect of genetic and genomic research. However, these sequence datasets contain quite a number of machine-induced errors-e.g. errors due to substitution can be as high as 2.5%. Existing error-correction methods are still far from perfect. In fact, more errors are sometimes...
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We study phylogenetic reconstruction of evolutionary trees, undergoing three possible types of mutations: substitutions, insertions, and deletions. We give the first efficient algorithm for this problem which needs sequences of only poly-logarithmic length. The best previously known result of Daskalakis and Roch [DR10] showed how to do phylogenetic reconstruction using sequences of polynomial l...
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A fundamental task in sequence analysis is to calculate the probability of a multiple alignment given a phylogenetic tree relating the sequences and an evolutionary model describing how sequences change over time. However, the most widely used phylogenetic models only account for residue substitution events. We describe a probabilistic model of a multiple sequence alignment that accounts for in...
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Insertion and deletion (INDEL) mutations, the most common type of structural variance, are associated with several human diseases. The detection of INDELs through next-generation sequencing (NGS) is becoming more common due to the decrease in costs, the increase in efficiency, and sensitivity improvements demonstrated by the various sequencing platforms and analytical tools. However, there are ...
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We investigate two generalizations of insertion and deletion of words, that have recently become of interest in the context of molecular computing. Given a pair of words (x, y), called a context, the (x, y)-contextual insertion of a word v into a word u is performed as follows. For each occurrence of xy as a subword in u, we include in the result of the contextual insertion the words obtained b...
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ژورنال
عنوان ژورنال: Scientific and Technical Journal of Information Technologies, Mechanics and Optics
سال: 2016
ISSN: 2226-1494
DOI: 10.17586/2226-1494-2016-16-1-108-114