Search Results - Burrows–Wheeler transform longest common prefix array multithreading parallel algorithms

Multithread Multistring Burrows–Wheeler Transform and Longest Common Prefix Array

Authors: Bonizzoni, Paola Della Vedova, Gianluca Pirola, Yuri et al.

Source: Journal of Computational Biology. 26:948-961

Subject Terms: Burrows-Wheeler transform, longest common prefix array, multithreading, parallel algorithms, Burrows–Wheeler transform longest common prefix array multithreading parallel algorithms, 0206 medical engineering, Computational Biology, 0102 computer and information sciences, 02 engineering and technology, Sequence Analysis, 01 natural sciences, Algorithms

File Description: application/pdf

Access URL: https://pubmed.ncbi.nlm.nih.gov/31140836
https://www.ncbi.nlm.nih.gov/pubmed/31140836
https://www.liebertpub.com/doi/10.1089/cmb.2018.0230
https://doi.org/10.1089/cmb.2018.0230
https://boa.unimib.it/handle/10281/265924
https://dblp.uni-trier.de/db/journals/jcb/jcb26.html#BonizzoniVPPR19
https://hdl.handle.net/10281/265924
https://doi.org/10.1089/cmb.2018.0230

Multithread multistring burrows-wheeler transform and longest common prefix array

Authors: Bonizzoni, P Della Vedova, G Pirola, Y et al.

Index Terms: Burrows-Wheeler transform, longest common prefix array, multithreading, parallel algorithm, Burrows–Wheeler transform longest common prefix array multithreading parallel algorithms, INF/01 - INFORMATICA, info:eu-repo/semantics/article

URL: http://hdl.handle.net/10281/265924
info:eu-repo/semantics/altIdentifier/pmid/31140836
info:eu-repo/semantics/altIdentifier/wos/WOS:000469491200001
volume:26
issue:9
firstpage:948
lastpage:961
numberofpages:14
journal:JOURNAL OF COMPUTATIONAL BIOLOGY

Enhancing Data Compression: Recent Innovations in LZ77 Algorithms.

Authors: Hong, Aaron Boucher, Christina

Source: Journal of Computational Biology; Aug2025, Vol. 32 Issue 8, p761-780, 20p

Fast Parallel Computation of Longest Common Prefixes.

Authors: Shun, Julian

Source: SC14: International Conference for High Performance Computing, Networking, Storage & Analysis; 2014, p387-398, 12p

Suffix sorting via matching statistics.

Authors: Lipták, Zsuzsanna Masillo, Francesco Puglisi, Simon J.

Source: Algorithms for Molecular Biology; 3/12/2024, Vol. 19 Issue 1, p1-18, 18p

Subject Terms: SUFFIXES & prefixes (Grammar), DATA structures, STATISTICS

Fast induced sorting suffixes on a multicore machine.

Authors: Lao, Bin Nong, Ge Chan, Wai Hong et al.

Source: Journal of Supercomputing; Jul2018, Vol. 74 Issue 7, p3468-3485, 18p

Subject Terms: SORTING (Electronic computers), MULTICORE processors, DATA compression, CENTRAL processing units, PARALLEL computers, ALGORITHMS

Using the Sadakane Compressed Suffix Tree to Solve the All-Pairs Suffix-Prefix Problem.

Authors: Rachid, Maan Haj Malluhi, Qutaibah Abouelhoda, Mohamed

Source: BioMed Research International; 2014, Vol. 2014, p1-11, 11p

GPU-based similarity metrics computation and machine learning approaches for string similarity evaluation in large datasets.

Authors: Baloi, Aurel Belean, Bogdan Turcu, Flaviu et al.

Source: Soft Computing - A Fusion of Foundations, Methodologies & Applications; Feb2024, Vol. 28 Issue 4, p3465-3477, 13p

Subject Terms: MACHINE learning, PARALLEL processing, GRAPHICS processing units, ELECTRONIC data processing, DIGITAL technology, COMPUTATIONAL complexity

Space-efficient computation of parallel approximate string matching.

Authors: Sadiq, Muhammad Umair Yousaf, Muhammad Murtaza

Source: Journal of Supercomputing; May2023, Vol. 79 Issue 8, p9093-9126, 34p

Subject Terms: PATTERN matching, DYNAMIC programming, VECTOR spaces, DNA sequencing, INFORMATION retrieval, NATURAL languages

EARRINGS: an efficient and accurate adapter trimmer entails no a priori adapter sequences.

Authors: Wang, Ting-Hsuan Huang, Cheng-Ching Hung, Jui-Hung

Source: Bioinformatics; 7/1/2021, Vol. 37 Issue 13, p1846-1852, 7p

Subject Terms: EARRINGS, A priori, SEQUENCE analysis, C++

A space-efficient solution to find the maximum overlap using a compressed suffix array.

Authors: Rachid, Maan Haj Malluhi, Qutaibah Abouelhoda, Mohamed

Source: 2nd Middle East Conference on Biomedical Engineering; 01/01/2014, p329-333, 5p

GSAlign: an efficient sequence alignment tool for intra-species genomes.

Authors: Lin, Hsin-Nan Hsu, Wen-Lian

Source: BMC Genomics; 2/24/2020, Vol. 21 Issue 1, p1-10, 10p, 3 Diagrams, 4 Charts, 1 Graph

Subject Terms: GENOMICS, COMPARATIVE genomics, SEQUENCE alignment, NUCLEOTIDE sequencing, GENOMES

3D-Stacked Many-Core Architecture for Biological Sequence Analysis Problems.

Authors: Liu, Pei Hemani, Ahmed Paul, Kolin et al.

Source: International Journal of Parallel Programming; Dec2017, Vol. 45 Issue 6, p1420-1460, 41p

Subject Terms: SEQUENCE analysis, APPLICATION-specific integrated circuits, COMPUTATIONAL biology, COPROCESSORS, THREE-dimensional integrated circuits, BIOINFORMATICS

MONI: A Pangenomic Index for Finding Maximal Exact Matches.

Authors: Rossi, Massimiliano Oliva, Marco Langmead, Ben et al.

Source: Journal of Computational Biology; Feb2022, Vol. 29 Issue 2, p169-187, 19p

Performance comparison of sequential and parallel compression applications for DNA raw data.

Authors: Guerra, Aníbal Lotero, Jaime Isaza, Sebastián

Source: Journal of Supercomputing; Dec2016, Vol. 72 Issue 12, p4696-4717, 22p

Subject Terms: DATA compression, SCALABILITY, RUN time systems (Computer science), COMPUTER storage capacity, BIOINFORMATICS

Evaluation of next-generation sequencing software in mapping and assembly.

Authors: Bao, Suying Jiang, Rui Kwan, WingKeung et al.

Source: Journal of Human Genetics; Jun2011, Vol. 56 Issue 6, p406-414, 9p, 5 Charts

Subject Terms: GENE mapping, NUCLEOTIDE sequence, BIOINFORMATICS, HUMAN genome, SOFTWARE sequencers, PERFORMANCE evaluation

Using GPUs for the Exact Alignment of Short-Read Genetic Sequences by Means of the Burrows-Wheeler Transform.

Authors: Salavert Torres, Jose Blanquer Espert, Ignacio Tomas Dominguez, Andres et al.

Source: IEEE/ACM Transactions on Computational Biology & Bioinformatics; Jul2012, Vol. 9 Issue 4, p1245-1256, 0p

Sublinear Computation Paradigm

Authors: Naoki Katoh Yuya Higashikawa Hiro Ito et al.

Resource Type: eBook.

Subjects: Computer algorithms--Mathematics, Big data

Categories: COMPUTERS / Computer Science, COMPUTERS / Programming / Algorithms

Long read alignment based on maximal exact match seeds.

Authors: Liu, Yongchao Schmidt, Bertil

Source: Bioinformatics; Sep2012, Vol. 28 Issue 18, pi318-i324, 1p

Subject Terms: SINGLE nucleotide polymorphisms, HUMAN genome, GERMINATION, SCALABILITY, PERFORMANCE evaluation, DATA analysis

Shared-Memory Parallelism Can Be Simple, Fast, and Scalable

Authors: Julian Shun

Resource Type: eBook.

Categories: COMPUTERS / Computer Architecture, COMPUTERS / Programming / Parallel, COMPUTERS / Programming / Algorithms