Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters
نویسندگان
چکیده
منابع مشابه
Improving Bloom Filter Performance on Sequence Data Using k-mer Bloom Filters
Using a sequence's k-mer content rather than the full sequence directly has enabled significant performance improvements in several sequencing applications, such as metagenomic species identification, estimation of transcript abundances, and alignment-free comparison of sequencing data. As k-mer sets often reach hundreds of millions of elements, traditional data structures are often impractical...
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a r t i c l e i n f o a b s t r a c t Bloom filters (BFs) are used in many applications for approximate check of set membership. Counting Bloom filters (CBFs) are an extension of BFs that enable the deletion of entries at the cost of additional storage requirements. Several alternatives to CBFs can be used to reduce the storage overhead. For example schemes based on d-left hashing or Cuckoo has...
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A Bloom filter is a compact data structure that supports membership queries on a set, allowing false positives. The simplicity and the excellent performance of a Bloom filter make it a standard data structure of great use in many network applications. In reducing the false positive rate of a Bloom filter, it is well known that the size of a Bloom filter and accordingly the number of hash indice...
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Bloom filters are heavily used in the literature for efficiently representing sets with elements from a large universe. However, the current literature lacks some important functionality on bloom filters which can be proven useful in several application domains, especially in distributed and P2P systems. This work presents some of these extensions. The work is motivated from our current researc...
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Bloom filters are used for answering queries on set membership. In this data structure, the whole element is not stored at the hashed address. Only a few bits are set in an array. Given a set S of cardinality n, we store it in an array of m bits using k hash functions h1(), . . . , hk(). Initially, all the cells in the array are set to 0. Then, for each element in the set, x ∈ S, for each 1 ≤ i...
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ژورنال
عنوان ژورنال: Journal of Computational Biology
سال: 2017
ISSN: 1557-8666
DOI: 10.1089/cmb.2016.0155