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Liu et al., 2014 - Google Patents

GPU-accelerated BWT construction for large collection of short reads

Liu et al., 2014

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Document ID
5186901058178007275
Author
Liu C
Luo R
Lam T
Publication year
Publication venue
arXiv preprint arXiv:1401.7457

External Links

Snippet

Advances in DNA sequencing technology have stimulated the development of algorithms and tools for processing very large collections of short strings (reads). Short-read alignment and assembly are among the most well-studied problems. Many state-of-the-art aligners, at …
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Classifications

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    • G06F17/00—Digital computing or data processing equipment or methods, specially adapted for specific functions
    • G06F17/30—Information retrieval; Database structures therefor; File system structures therefor
    • G06F17/30286—Information retrieval; Database structures therefor; File system structures therefor in structured data stores
    • G06F17/30312—Storage and indexing structures; Management thereof
    • G06F17/30321—Indexing structures
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
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    • G06F17/30961—Trees
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    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
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    • G06F17/30153—Redundancy elimination performed by the file system using compression, e.g. sparse files
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    • G06F17/30964—Querying
    • G06F17/30979—Query processing
    • G06F17/30985—Query processing by using string matching techniques
    • G—PHYSICS
    • G06—COMPUTING; CALCULATING; COUNTING
    • G06F—ELECTRICAL DIGITAL DATA PROCESSING
    • G06F19/00—Digital computing or data processing equipment or methods, specially adapted for specific applications
    • G06F19/10—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology
    • G06F19/22—Bioinformatics, i.e. methods or systems for genetic or protein-related data processing in computational molecular biology for sequence comparison involving nucleotides or amino acids, e.g. homology search, motif or SNP [Single-Nucleotide Polymorphism] discovery or sequence alignment
    • G—PHYSICS
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    • G06F9/00—Arrangements for programme control, e.g. control unit
    • G06F9/06—Arrangements for programme control, e.g. control unit using stored programme, i.e. using internal store of processing equipment to receive and retain programme
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