Results 11 to 20 of about 3,800 (211)
The Computer Journal, 2017 Accepted to The Computer Journal.
Andrea Farruggia +4 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
Navarro G. +6 more
core +2 more sources
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
doaj +2 more sources
Fully compressed suffix trees [PDF]
ACM Transactions on Algorithms, 2008 Suffix trees are by far the most important data structure in stringology, with a myriad of applications in fields like bioinformatics and information retrieval. Classical representations of suffix trees require Θ( n log n ) bits of space, for a string of size n .
Luís M. S. Russo +2 more
core +5 more sources
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
doaj +2 more sources
Efficient computation of absent words in genomic sequences [PDF]
BMC Bioinformatics, 2008 Background Analysis of sequence composition is a routine task in genome research. Organisms are characterized by their base composition, dinucleotide relative abundance, codon usage, and so on.
Herold Julia +2 more
doaj +3 more sources
40 years of suffix trees [PDF]
Communications of the ACM, 2016 Tracing the first four decades in the life of suffix trees, their many incarnations, and their applications.
Alberto Apostolico +4 more
openaire +5 more sources
Converting suffix trees into factor/suffix oracles [PDF]
Journal of Discrete Algorithms, 2008 Several methods to compress suffix trees were defined, most of them with the aim of obtaining compact (that is, space economical) index structures. Besides this practical aspect, a compression method can reveal structural properties of the resulting data structure, allowing a better understanding of it and a better estimation of its performances.
Rusu, Irena
openaire +4 more sources
Weighted Ancestors in Suffix Trees [PDF]
, 2014 The classical, ubiquitous, predecessor problem is to construct a data structure for a set of integers that supports fast predecessor queries. Its generalization to weighted trees, a.k.a. the weighted ancestor problem, has been extensively explored and successfully reduced to the predecessor problem.
Gawrychowski, P. +2 more
openaire +5 more sources
Faster suffix tree construction with missing suffix links [PDF]
Proceedings of the thirty-second annual ACM symposium on Theory of computing, 2000 Summary: We consider suffix tree construction for situations with missing suffix links. Two examples of such situations are suffix trees for parameterized strings and suffix trees for two-dimensional arrays. These trees also have the property that the node degrees may be large.
Cole, Richard, Hariharan, Ramesh
core +7 more sources