Fast index based algorithms and software for matching position specific scoring matrices
BMC Bioinformatics, 2006 Background In biological sequence analysis, position specific scoring matrices (PSSMs) are widely used to represent sequence motifs in nucleotide as well as amino acid sequences.
Homann Robert +3 more
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SArKS: de novo discovery of gene expression regulatory motif sites and domains by suffix array kernel smoothing. [PDF]
Bioinformatics, 2019 Wylie DC, Hofmann HA, Zemelman BV.
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Compressed Suffix Arrays for Massive Data [PDF]
, 2009 We present a fast space-efficient algorithm for constructing compressed suffix arrays (CSA). The algorithm requires O (n logn ) time in the worst case, and only O (n ) bits of extra space in addition to the CSA. As the basic step, we describe an algorithm for merging two CSAs.
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RIsearch2: suffix array-based large-scale prediction of RNA-RNA interactions and siRNA off-targets. [PDF]
Nucleic Acids Res, 2017 Alkan F +7 more
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SA-SSR: a suffix array-based algorithm for exhaustive and efficient SSR discovery in large genetic sequences. [PDF]
Bioinformatics, 2016 Pickett BD +7 more
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Linear-time computation of minimal absent words using suffix array. [PDF]
BMC Bioinformatics, 2014 Barton C +3 more
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Linear-time Suffix Sorting - A New Approach for Suffix Array Construction [PDF]
, 2016 Baier, Uwe
core +1 more source
Acceleration of short and long DNA read mapping without loss of accuracy using suffix array. [PDF]
Bioinformatics, 2014 Tárraga J +8 more
europepmc +1 more source
Suffix arrays in theory and practice.
, 2007 The suffix array of a string is a permutation of all starting positions of the string's suffixes in lexicographical order. In this thesis, we investigate mathematical and algorithmical aspects of suffix arrays. The first part mainly deals with combinatorial properties of suffix arrays and their enumeration.
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mkESA: enhanced suffix array construction tool. [PDF]
Bioinformatics, 2009 Homann R +3 more
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