rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
نویسندگان
چکیده
منابع مشابه
rasbhari: Optimizing Spaced Seeds for Database Searching, Read Mapping and Alignment-Free Sequence Comparison
Many algorithms for sequence analysis rely on word matching or word statistics. Often, these approaches can be improved if binary patterns representing match and don't-care positions are used as a filter, such that only those positions of words are considered that correspond to the match positions of the patterns. The performance of these approaches, however, depends on the underlying patterns....
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The advent of high-throughput sequencing technologies constituted a major advance in genomic studies, offering new prospects in a wide range of applications.We propose a rigorous and flexible algorithmic solution to mapping SOLiD color-space reads to a reference genome. The solution relies on an advanced method of seed design that uses a faithful probabilistic model of read matches and, on the ...
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MOTIVATION Alignment-free methods for sequence comparison are increasingly used for genome analysis and phylogeny reconstruction; they circumvent various difficulties of traditional alignment-based approaches. In particular, alignment-free methods are much faster than pairwise or multiple alignments. They are, however, less accurate than methods based on sequence alignment. Most alignment-free ...
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Alignment-free methods are increasingly used for genome analysis and phylogeny reconstruction since they circumvent various difficulties of traditional approaches that rely on multiple sequence alignments. In particular, they are much faster than alignment-based methods. Most alignmentfree approaches work by analyzing the k-mer composition of sequences. In this paper, we propose to use ‘spaced ...
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We review recent developments in spaced seed design for cross-species sequence alignment. We start with a brief overview of original ideas and early techniques, and then focus on more recent work on finding accurate (sensitive and specific) seeds for cross-species cDNA-to-genome alignment. These recent developments include methods and models for estimating seed specificity and determining sensi...
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ژورنال
عنوان ژورنال: PLOS Computational Biology
سال: 2016
ISSN: 1553-7358
DOI: 10.1371/journal.pcbi.1005107