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Parallel Processing of Multiple Pattern Matching Algorithms for Biological Sequences: Methods and Performance Results

https://doi.org/10.5772/18488
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/pmic.200300511openalex-snapshot
Proteogenomic mapping as a complementary method to perform genome annotation
inferredcites →https://doi.org/10.1002/spe.4380100608openalex-snapshot
Practical fast searching in strings
inferredcites →https://doi.org/10.1007/3-540-09510-1_10openalex-snapshot
A string matching algorithm fast on the average
inferredcites →https://doi.org/10.1007/3-540-45009-2_12openalex-snapshot
Is the Schedule Clause Really Necessary in OpenMP?
inferredcites →https://doi.org/10.1007/3-540-47849-3_18openalex-snapshot
Factor Oracle: A New Structure for Pattern Matching
inferredcites →https://doi.org/10.1007/3-540-61258-0_7openalex-snapshot
Approximate multiple string search
inferredcites →https://doi.org/10.1007/978-3-540-77048-0_16openalex-snapshot
MDH: A High Speed Multi-phase Dynamic Hash String Matching Algorithm for Large-Scale Pattern Set
inferredcites →https://doi.org/10.1007/bf01185427openalex-snapshot
Speeding up two string-matching algorithms
inferredcites →https://doi.org/10.1007/bfb0030778openalex-snapshot
A bit-parallel approach to suffix automata: Fast extended string matching
inferredcites →https://doi.org/10.1016/0898-1221(95)90197-3openalex-snapshot
PVM: Parallel virtual machine: A users' guide and tutorial for networked parallel computing
inferredcites →https://doi.org/10.1016/j.compbiomed.2003.11.003openalex-snapshot
On exact string matching of unique oligonucleotides
inferredcites →https://doi.org/10.1016/j.jcss.2004.12.003openalex-snapshot
Designing seeds for similarity search in genomic DNA
inferredcites →https://doi.org/10.1016/s0020-0190(99)00092-7openalex-snapshot
Fast practical multi-pattern matching
inferredcites →https://doi.org/10.1016/s0167-739x(03)00109-2openalex-snapshot
Performance evaluation of load balancing strategies for approximate string matching application on an MPI cluster of heterogeneous workstations
inferredcites →https://doi.org/10.1063/1.4823450openalex-snapshot
PVM-Parallel Virtual Machine: AUsers' Guide and Tutorial for Networked Parallel Computing
inferredcites →https://doi.org/10.1093/bioinformatics/bti224openalex-snapshot
SITEBLAST-rapid and sensitive local alignment of genomic sequences employing motif anchors
inferredcites →https://doi.org/10.1093/nar/gkh361openalex-snapshot
The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences
inferredcites →https://doi.org/10.1109/csb.2002.1039337openalex-snapshot
Fast and sensitive alignment of large genomic sequences
inferredcites →https://doi.org/10.1109/fpt.2006.270297openalex-snapshot
Generating hardware from OpenMP programs
inferredcites →https://doi.org/10.1145/1187436.1187438openalex-snapshot
Multipattern string matching with q -grams
inferredcites →https://doi.org/10.1145/135239.135243openalex-snapshot
A new approach to text searching
inferredcites →https://doi.org/10.1145/360825.360855openalex-snapshot
Efficient string matching
inferredcites →https://doi.org/10.1145/75335.75352openalex-snapshot
A new approach to text searching
inferredcites →https://doi.org/10.1147/rd.312.0249openalex-snapshot
Efficient randomized pattern-matching algorithms
inferredcites →https://doi.org/10.1177/016555158801400604openalex-snapshot
Efficiency of text scanning in bibliographic databases using microprocessor-based, multiprocessor networks
inferredcites →https://doi.org/10.1177/102831538801400604openalex-snapshot
Efficiency of text scanning in bibliographic databases using microprocessor-based, multiprocessor networks
inferredcites →https://doi.org/10.1186/1748-7188-2-13openalex-snapshot
Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules
inferredcites →https://doi.org/10.5220/0003133202740277openalex-snapshot
EXPERIMENTAL RESULTS ON MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES
inferredcites →https://doi.org/10.5860/choice.32-5696openalex-snapshot
Text algorithms
inferredcites →https://doi.org/10.5860/choice.42-0990openalex-snapshot
Introduction to parallel computing

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/978-3-319-24584-3_102openalex-snapshot
Parallel GPU-Based Hybrid String Matching Algorithm
inferred← citeshttps://doi.org/10.1007/s10586-019-02955-9openalex-snapshot
KPN-based parallelization of Wu–Manber algorithm on multi-core machines
inferred← citeshttps://doi.org/10.1007/s13369-020-05310-yopenalex-snapshot
Design and Analysis of Pattern Matching Algorithms Based on QuRAM Processing
inferred← citeshttps://doi.org/10.1142/s0218213015400011openalex-snapshot
A Hybrid Parallel Implementation of the Aho–Corasick and Wu–Manber Algorithms Using NVIDIA CUDA and MPI Evaluated on a Biological Sequence Database
inferred← citeshttps://doi.org/10.12681/eadd/29868openalex-snapshot
Parallel and distributed implementations of multiple and two-dimensional pattern matching algorithms
inferred← citeshttps://doi.org/10.4236/jcc.2016.413001openalex-snapshot
Parallel Quick Search Algorithm for the Exact String Matching Problem Using OpenMP
inferred← citeshttps://doi.org/10.5220/0003769801820187openalex-snapshot
PERFORMANCE STUDY OF PARALLEL HYBRID MULTIPLE PATTERN MATCHING ALGORITHMS FOR BIOLOGICAL SEQUENCES
inferred← citeshttps://doi.org/10.7287/peerj-cs.957v0.1/reviews/1openalex-snapshot
Peer Review #1 of "Quantum-effective exact multiple patterns matching algorithms for biological sequences (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj-cs.957v0.1/reviews/2openalex-snapshot
Peer Review #2 of "Quantum-effective exact multiple patterns matching algorithms for biological sequences (v0.1)"
inferred← citeshttps://doi.org/10.7287/peerj-cs.957v0.2/reviews/1openalex-snapshot
Peer Review #1 of "Quantum-effective exact multiple patterns matching algorithms for biological sequences (v0.2)"
inferred← citeshttps://doi.org/10.7287/peerj-cs.957v0.3/reviews/1openalex-snapshot
Peer Review #1 of "Quantum-effective exact multiple patterns matching algorithms for biological sequences (v0.3)"
inferred← citeshttps://doi.org/10.7717/peerj-cs.957openalex-snapshot
Quantum-effective exact multiple patterns matching algorithms for biological sequences
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