Cache-oblivious dynamic programming for bioinformatics

IEEE/ACM Transactions on Computational Biology and Bioinformatics

Volumn 7, Issue 3, 2010, Pages 495-510

  Chowdhury, Rezaul Alan ^a   Le, Hai Son ^b   Ramachandran, Vijaya ^c  

^a UNIVERSITY OF TEXAS AT AUSTIN   (United States)

^b Carnegie Mellon University ^*  (United States)

^c University of Texas at Austin   (United States)

Author keywords

Analysis of Algorithms and Problem Complexity; Biology and genetics; cache efficient; cache oblivious.; Combinatorial algorithms; dynamic programming; median; RNA secondary structure prediction; Sequence alignment; Theory of Computation; Tradeoffs between Complexity Measures

Indexed keywords

ANALYSIS OF ALGORITHMS; BIOLOGY AND GENETICS; CACHE-EFFICIENT; CACHE-OBLIVIOUS; COMBINATORIAL ALGORITHM; COMPLEXITY MEASURES; PROBLEM COMPLEXITY; RNA SECONDARY STRUCTURE PREDICTION; SEQUENCE ALIGNMENTS; THEORY OF COMPUTATION;

ALGORITHMS; ALIGNMENT; BIOINFORMATICS; CACHE MEMORY; CHROMOSOMES; COMBINATORIAL MATHEMATICS; COMPUTATION THEORY; DYNAMIC PROGRAMMING; FORECASTING; RNA;

COMPUTATIONAL EFFICIENCY;

RNA;

ALGORITHM; ARTICLE; BASE PAIRING; BIOLOGY; CHEMISTRY; COMPUTER PROGRAM; CONFORMATION; METHODOLOGY; NUCLEOTIDE SEQUENCE; SEQUENCE ALIGNMENT;

ALGORITHMS; BASE PAIRING; BASE SEQUENCE; COMPUTATIONAL BIOLOGY; NUCLEIC ACID CONFORMATION; RNA; SEQUENCE ALIGNMENT; SOFTWARE;

EID: 77955467765     PISSN: 15455963     EISSN: None     Source Type: Journal    
DOI: 10.1109/TCBB.2008.94     Document Type: Article

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