Results 141 to 150 of about 4,504,185 (191)
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Simpler FM-index for parameterized string matching
Information Processing Letters, 2021In parameterized string matching, a string comprises static and parameterized symbols. Two strings are said to be matched if there exists a one-to-one mapping of parameterized symbols onto itself such that it transforms one string into the other ...
Sung-Hwan Kim, Hwan-Gue Cho
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Memory–Efficient FM-Index Construction for Reference Genomes
2022 IEEE International Conference on Bioinformatics and Biomedicine (BIBM), 2022FM-index is traditionally constructed over the forward strand complemented with the reverse strand to support searching both strands by executing a single procedure. Although it expedite the process of indexing, it consumes large amount of memory.
A. K. Das +2 more
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International Conference -Beyond Databases, Architectures, and Structures, 2015 The FM-index is a celebrated compressed data structure for full-text pattern searching. After the first wave of interest in its theoretical developments, we can observe a surge of interest in practical FM-index variants in the last few years.
S. Grabowski +2 more
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Accelerating FM-index Search for Genomic Data Processing
Proceedings of the 47th International Conference on Parallel Processing, 2018The deluge of genomics data is incurring prohibitively high computational costs. As an important building block for genomic data processing algorithms, FM-index search occupies most of execution time in sequence alignment. Due to massive random streaming
Yuanrong Wang +4 more
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Simple Runs-Bounded FM-Index Designs Are Fast
The Sea, 2023 Peer ...
Diego Díaz-Domínguez +3 more
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FM-Index Reveals the Reverse Suffix Array
Annual Symposium on Combinatorial Pattern Matching, 2020 Given a text T[1,n] over an alphabet Σ of size σ, the suffix array of T stores the lexicographic order of the suffixes of T. The suffix array needs Θ(nlog n) bits of space compared to the n log σ bits needed to store T itself. A major breakthrough [FM - Index, FOCS'00] in the last two decades has been encoding the suffix array in near-optimal number of
Arnab Ganguly +6 more
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A novel fast multiple nucleotide sequence alignment method based on FM-index
Briefings in Bioinformatics, 2021 AbstractMultiple sequence alignment (MSA) is fundamental to many biological applications. But most classical MSA algorithms are difficult to handle large-scale multiple sequences, especially long sequences. Therefore, some recent aligners adopt an efficient divide-and-conquer strategy to divide long sequences into several short sub-sequences. Selecting
Huan Liu, Q. Zou, Yun Xu
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Workshop on Algorithm Engineering and Experimentation, 2015 Hongwei Huo +5 more
semanticscholar +2 more sources
IEEE Transactions on Biomedical Circuits and Systems, 2023
This article presents an Ferragina-Manzini index (FM-index) based paired-end short-read mapping hardware accelerator. Four techniques are proposed to significantly reduce the number of memory accesses and operations to improve the throughput.
Chung-Hsuan Yang +5 more
semanticscholar +1 more source
This article presents an Ferragina-Manzini index (FM-index) based paired-end short-read mapping hardware accelerator. Four techniques are proposed to significantly reduce the number of memory accesses and operations to improve the throughput.
Chung-Hsuan Yang +5 more
semanticscholar +1 more source