Results 1 to 10 of about 40,634 (160)
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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Statistical signature of subtle behavioral changes in large-scale assays. [PDF]
PLoS Computational BiologyThe central nervous system can generate various behaviors, including motor responses, which we can observe through video recordings. Recent advances in gene manipulation, automated behavioral acquisition at scale, and machine learning enable us to ...
Alexandre Blanc +12 more
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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
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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
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Average profiles, from tries to suffix-trees [PDF]
Discrete Mathematics & Theoretical Computer Science, 2005 We build upon previous work of Fayolle (2004) and Park and Szpankowski (2005) to study asymptotically the average internal profile of tries and of suffix-trees. The binary keys and the strings are built from a Bernoulli source $(p,q)$.
Pierre Nicodème
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Analysis of the multiplicity matching parameter in suffix trees [PDF]
Discrete Mathematics & Theoretical Computer Science, 2005 In a suffix tree, the multiplicity matching parameter (MMP) $M_n$ is the number of leaves in the subtree rooted at the branching point of the $(n+1)$st insertion.
Mark Daniel Ward, Wojciech Szpankowski
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Non-Overlapping LZ77 Factorization and LZ78 Substring Compression Queries with Suffix Trees
Algorithms, 2021 We present algorithms computing the non-overlapping Lempel–Ziv-77 factorization and the longest previous non-overlapping factor table within small space in linear or near-linear time with the help of modern suffix tree representations fitting into ...
Dominik Köppl
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A tight upper bound on the size of the antidictionary of a binary string [PDF]
Discrete Mathematics & Theoretical Computer Science, 2005 A tight upper bound of the size of the antidictionary of a binary string is presented. And it is shown that the size of the antidictionary of a binary sting is always smaller than or equal to that of its dictionary.
Hiroyoshi Morita, Takahiro Ota
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On the Number of 2-Protected Nodes in Tries and Suffix Trees [PDF]
Discrete Mathematics & Theoretical Computer Science, 2012 We use probabilistic and combinatorial tools on strings to discover the average number of 2-protected nodes in tries and in suffix trees. Our analysis covers both the uniform and non-uniform cases.
Jeffrey Gaither +3 more
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