Mismatch-tolerant, alignment-free sequence classification using multiple spaced seeds and multiindex Bloom filters
نویسندگان
چکیده
منابع مشابه
Fast alignment-free sequence comparison using spaced-word frequencies
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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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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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...
متن کاملClassification of DNA sequences using Bloom filters
MOTIVATION New generation sequencing technologies producing increasingly complex datasets demand new efficient and specialized sequence analysis algorithms. Often, it is only the 'novel' sequences in a complex dataset that are of interest and the superfluous sequences need to be removed. RESULTS A novel algorithm, fast and accurate classification of sequences (FACSs), is introduced that can a...
متن کاملAlignment-free sequence comparison with spaced k-mers
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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ژورنال
عنوان ژورنال: Proceedings of the National Academy of Sciences
سال: 2020
ISSN: 0027-8424,1091-6490
DOI: 10.1073/pnas.1903436117