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Practical Compressed Suffix Trees [PDF]
Algorithms, 2013 The suffix tree is an extremely important data structure in bioinformatics. Classical implementations require much space, which renders them useless to handle large sequence collections. Recent research has obtained various compressed representations for
G Navarro +2 more
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PFP Compressed Suffix Trees. [PDF]
Proc Worksh Algorithm Eng Exp, 2021 Prefix-free parsing (PFP) was introduced by Boucher et al. (2019) as a preprocessing step to ease the computation of Burrows-Wheeler Transforms (BWTs) of genomic databases. Given a string S, it produces a dictionary D and a parse P of overlapping phrases such that BWT(S) can be computed from D and P in time and workspace bounded in terms of their ...
Boucher C +6 more
europepmc +6 more sources
Distributed suffix trees [PDF]
Journal of Discrete Algorithms, 2005 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Raphaël Clifford
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DTA-SiST: de novo transcriptome assembly by using simplified suffix trees [PDF]
BMC Bioinformatics, 2019 Background Alternative splicing allows the pre-mRNAs of a gene to be spliced into various mRNAs, which greatly increases the diversity of proteins. High-throughput sequencing of mRNAs has revolutionized our ability for transcripts reconstruction. However,
Jin Zhao +4 more
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A novel linear indexing method for strings under all internal nodes in a suffix tree [PDF]
Frontiers in BioinformaticsSuffix trees are fundamental data structures in stringology and have wide applications across various domains. In this work, we propose two linear-time algorithms for indexing strings under each internal node in a suffix tree while preserving the ability
Anas Al-okaily, Abdelghani Tbakhi
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Reversed Lempel–Ziv Factorization with Suffix Trees
Algorithms, 2021 We present linear-time algorithms computing the reversed Lempel–Ziv factorization [Kolpakov and Kucherov, TCS’09] within the space bounds of two different suffix tree representations.
Dominik Köppl
exaly +3 more sources
Replacing suffix trees with enhanced suffix arrays
Journal of Discrete Algorithms, 2004 zbMATH Open Web Interface contents unavailable due to conflicting licenses.
Stefan Kurtz, Enno Ohlebusch
exaly +2 more sources
A suffix tree or not a suffix tree? [PDF]
Journal of Discrete Algorithms, 2015 Full version.
Starikovskaya, Tatiana A. +1 more
openaire +5 more sources
Analysis of the average depth in a suffix tree under a Markov model [PDF]
Discrete Mathematics & Theoretical Computer Science, 2005 In this report, we prove that under a Markovian model of order one, the average depth of suffix trees of index n is asymptotically similar to the average depth of tries (a.k.a. digital trees) built on n independent strings.
Julien Fayolle, Mark Daniel Ward
doaj +1 more source