Results 11 to 20 of about 14,465 (182)
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms, 2004 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Abouelhoda, Mohamed Ibrahim +2 more
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A quick tour on suffix arrays and compressed suffix arrays
Theoretical Computer Science, 2011 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Roberto Grossi
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On the combinatorics of suffix arrays [PDF]
, 2012 We prove several combinatorial properties of suffix arrays, including a characterization of suffix arrays through a bijection with a certain well-defined class of permutations. Our approach is based on the characterization of Burrows-Wheeler arrays given
Kucherov, Gregory +2 more
core +5 more sources
Dynamic extended suffix arrays
Journal of Discrete Algorithms, 2010 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Salson, Mikael +3 more
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GHOSTX: an improved sequence homology search algorithm using a query suffix array and a database suffix array. [PDF]
PLoS ONE, 2014 DNA sequences are translated into protein coding sequences and then further assigned to protein families in metagenomic analyses, because of the need for sensitivity.
Shuji Suzuki +3 more
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Generalized enhanced suffix array construction in external memory
Algorithms for Molecular Biology, 2017 Background Suffix arrays, augmented by additional data structures, allow solving efficiently many string processing problems. The external memory construction of the generalized suffix array for a string collection is a fundamental task when the size of ...
Felipe A. Louza +3 more
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Suffix-Sorting via Shannon-Fano-Elias Codes
Algorithms, 2010 Given a sequence T = t0t1 . . . tn-1 of size n = |T|, with symbols from a fixed alphabet Σ, (|Σ| ≤ n), the suffix array provides a listing of all the suffixes of T in a lexicographic order.
Donald Adjeroh, Fei Nan
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On the suitability of suffix arrays for lempel-ziv data compression [PDF]
, 2009 Lossless compression algorithms of the Lempel-Ziv (LZ) family are widely used nowadays. Regarding time and memory requirements, LZ encoding is much more demanding than decoding.
D. Gusfield +9 more
core +2 more sources
TOPAZ: asymmetric suffix array neighbourhood search for massive protein databases
BMC Bioinformatics, 2018 Background Protein homology search is an important, yet time-consuming, step in everything from protein annotation to metagenomics. Its application, however, has become increasingly challenging, due to the exponential growth of protein databases.
Alan Medlar, Liisa Holm
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Designing small universal k-mer hitting sets for improved analysis of high-throughput sequencing. [PDF]
PLoS Computational Biology, 2017 With the rapidly increasing volume of deep sequencing data, more efficient algorithms and data structures are needed. Minimizers are a central recent paradigm that has improved various sequence analysis tasks, including hashing for faster read overlap ...
Yaron Orenstein +4 more
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