Results 11 to 20 of about 14,384 (164)
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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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
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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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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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Fast mapping of short sequences with mismatches, insertions and deletions using index structures. [PDF]
PLoS Computational Biology, 2009 With few exceptions, current methods for short read mapping make use of simple seed heuristics to speed up the search. Most of the underlying matching models neglect the necessity to allow not only mismatches, but also insertions and deletions.
Steve Hoffmann +7 more
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Scalable Parallel Suffix Array Construction [PDF]
Parallel Computing, 2006 Suffix arrays are a simple and powerful data structure for text processing that can be used for full text indexes, data compression, and many other applications in particular in bioinformatics. We describe the first implementation and experimental evaluation of a scalable parallel algorithm for suffix array construction.
Kulla, F., Sanders, P.
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