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A Framework for Space-Efficient String Kernels
2017
Algorithmica
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Versatile succinct representations of the bidirectional Burrows-Wheeler transform. ESA 2013. D. Belazzougui, G. Navarro, D. Valenzuela. Improved compressed indexes for full-text document retrieval. ...
O(n log log σ) Burrows-Wheeler tr. [1] D. Belazzougui. Linear time construction of compressed text indices in compact space. STOC 2014. [2] D. Belazzougui, G. Navarro, D. Valenzuela. ...
doi:10.1007/s00453-017-0286-4
fatcat:e2r44hskgrhfvo4f6who3fphgi
25 Years of the Burrows-Wheeler Transform (Dagstuhl Seminar 19241)
2019
Dagstuhl Reports
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Dagstuhl Seminar 19241 ("25 Years of the Burrows-Wheeler Transform") took place from June 10th to 14th, 2019, and was attended by 45 people from 13 countries and the three fields of Algorithms and Data ...
Feedback was generally positive and we are confident the seminar fostered interdisciplinary connections and will eventually result in noteworthy joint publications. License Creative Commons BY 3.0 ...
We present an index data structure for the bijective Burrows-Wheeler transform [1] . The index data structure is based on the FM index [2] . ...
doi:10.4230/dagrep.9.6.55
dblp:journals/dagstuhl-reports/GagieMNS19
fatcat:vw3nruzqkzbrdi3rpxpqtjkosa
Wavelet Trees for All
[chapter]
2012
Lecture Notes in Computer Science
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There exists a (1D) RMQ structure that, on array A[1, n] of numbers, Requires 2n + o(n) bits of space. Answers queries in constant time. Does not access A. ...
Discrete Grids Use a wavelet tree for the points. Store the values aligned to the root bitmap, in V [1, n]. We store a one-dimensional RMQ structure per wavelet tree node, for V v [1, n v ]. ...
and visibility reduce
A B B B B B B B B C C C C C C C C C D D D D D D D D
Full-text IndexesA way to simulate the suffix array A[1, n] in little space uses the Burrows-Wheeler Transform (BWT) of T ...
doi:10.1007/978-3-642-31265-6_2
fatcat:najqyrywlrezdofzr7c674olnm
Wavelet trees for all
2014
Journal of Discrete Algorithms
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There exists a (1D) RMQ structure that, on array A[1, n] of numbers, Requires 2n + o(n) bits of space. Answers queries in constant time. Does not access A. ...
Discrete Grids Use a wavelet tree for the points. Store the values aligned to the root bitmap, in V [1, n]. We store a one-dimensional RMQ structure per wavelet tree node, for V v [1, n v ]. ...
and visibility reduce
A B B B B B B B B C C C C C C C C C D D D D D D D D
Full-text IndexesA way to simulate the suffix array A[1, n] in little space uses the Burrows-Wheeler Transform (BWT) of T ...
doi:10.1016/j.jda.2013.07.004
fatcat:43562tjtr5fajgr4nue4zcteei
Computation over Compressed Structured Data (Dagstuhl Seminar 16431)
2017
Dagstuhl Reports
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This report documents the program and the outcomes of Dagstuhl Seminar 16431 "Computation over Compressed Structured Data". ...
We plan to combine the recently proposed GLOUDS representation [1] with DSM, a technique used to compress Web and social graphs by exploiting the presence of bicliques and dense subgraphs [2]. ...
Since GLOUDS benefits from a representation with fewer edges per node and DSM reduces the number of edges from m * n to m + n when representing an (m, n)-biclique, we believe the combination can lead to ...
doi:10.4230/dagrep.6.10.99
dblp:journals/dagstuhl-reports/BilleLMN16
fatcat:jel4wyc2gje6thmu5zj7aryofu
Linear-time string indexing and analysis in small space
[article]
2016
arXiv
pre-print
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on the Burrows-Wheeler transform (BWT) have been developed, all taking an amount of space that is close to the input size in bits. ...
The field of succinct data structures has flourished over the last 16 years. ...
Acknowledgement The authors wish to thank Travis Gagie for explaining the data structure built in Lemma 33, as well as for valuable comments and encouragements, Gonzalo Navarro for explaining the algorithm ...
arXiv:1609.06378v1
fatcat:nwtoh4rvmjcjle2oe4u3c3byie
GraphAligner: Rapid and Versatile Sequence-to-Graph Alignment
[article]
2019
bioRxiv
pre-print
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Compared to state-of-the-art tools, GraphAligner is 12x faster and uses 5x less memory, making it as efficient as aligning reads to linear reference genomes. ...
Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pan-genome graph. ...
Availability of data and materials ...
doi:10.1101/810812
fatcat:mksvk7jfyngyte4n6esa54qb4q
GraphAligner: rapid and versatile sequence-to-graph alignment
2020
Genome Biology
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Compared to the state-of-the-art tools, GraphAligner is 13x faster and uses 3x less memory. ...
Aligning sequences to genome graphs is key to many applications, including error correction, genome assembly, and genotyping of variants in a pangenome graph. ...
The source code of GraphAligner is available on GitHub [67] . The source code of GraphAligner version 1.0.11 used in the experiments is available on Zenodo [68] ...
doi:10.1186/s13059-020-02157-2
pmid:32972461
fatcat:sxz4jkj4crgdxi2oc4h4kr7iem
Time- and Space-Efficient Regular Path Queries on Graphs
[article]
2021
arXiv
pre-print
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We combine a bit-parallel simula-tion of the Glushkov automaton of the regular expression with thering index introduced by Arroyuelo et al., exploiting its wavelettree representation of the triples in ...
order to efficiently reach thestates of the product graph that are relevant for the query. ...
The concatenation 𝐿 o • 𝐿 s • 𝐿 p is indeed the Burrows-Wheeler Transform (BWT) [9] of the concatenation of all the triples (with some tweaks, see the original article [4] for details). ...
arXiv:2111.04556v1
fatcat:jmnlkleovbcq3gxu3hdm63hvgu
Sequence to graph alignment : theory, practice and applications
[article]
2020
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One representation of pangenomes is the sequence graph or the pangenome graph, which uses a graph format to represent genetic diversity. ...
To show the utility of GraphAligner, I present a long read genotyping pipeline, and an error correction pipeline that outperforms existing tools by a factor of two in correction accuracy and an order of ...
A Wheeler graph is essentially a generalization of the Burrows-Wheeler transform to graphs, and any linear string can be considered a linear Wheeler graph. ...
doi:10.22028/d291-32061
fatcat:vvpwnf6ejvbc5oeabusfflxqc4
Dagstuhl Reports, Volume 9, Issue 6, June 2019, Complete Issue
[article]
2020
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The vision of Real VR is enabling to experience movies, concerts, even live sports events in HMDs with the sense of immersion of really "being-there", unattainable by today's technologies. ...
the state-of-the-art, current challenges, as well as promising future research directions in Real VR. ...
In recent years several compressed indexes based on variants of the Burrows-Wheeler transformation have been introduced. ...
doi:10.4230/dagrep.9.6
fatcat:3w3rearmjrdejkbazhpjqmucde
Approaches to genome analysis through the application of graph theory
2021
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Over the past twenty years the cost of genome sequencing has dropped from a prohibitive amount of hundreds of millions of dollars, to just a few thousand dollars. ...
Partial, ad-hoc solutions, such as the introduction of alternative sequences for sections of the genome, have provided a stopgap but fail to fully represent the wealth of information now known about the ...
Burrows Wheeler Transform In situations where there is a very small alphabet size compared to the length of the string, a suffix array can occupy more space than the original string. ...
doi:10.14288/1.0401888
fatcat:hy7riaj4ajbsbhkcjr3pkftb7a
Approximate string matching for high-throughput sequencing
[article]
2015
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The ability to assess the content of a DNA sample at base-level resolution opens the way to a myriad of applications, including individual genotyping and assessment of large structural variations, measurement ...
To the best of my knowledge, this is the first study providing a comprehensive exposition, implementation and evaluation of such methods. ...
Succinct full-text indices The Burrows-Wheeler transform (BWT) [Burrows and Wheeler, 1994 ] is a transformation de ining a permutation of an input string. ...
doi:10.17169/refubium-15562
fatcat:opflq33mv5ewbkxkaokacdwlx4