Results 31 to 40 of about 58,956 (207)
Computational and Structural Biotechnology Journal, 2022 Multiple DNA/RNA sequence alignment is an important fundamental tool in bioinformatics, especially for phylogenetic tree construction. With DNA-sequencing improvements, the amount of bioinformatics data is constantly increasing, and various tools need to
Ziyuan Wang +7 more
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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
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Pattern Matching on Sparse Suffix Trees [PDF]
, 2011 International audienceWe consider a compact text index based on evenly spaced sparse suffix trees of a text [9]. Such a tree is defined by partitioning the text into blocks of equal size and constructing the suffix tree only for those suffixes that start
Kolpakov, Roman +2 more
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Shortest Unique Substring Query Revisited [PDF]
, 2014 We revisit the problem of finding shortest unique substring (SUS) proposed recently by [6]. We propose an optimal $O(n)$ time and space algorithm that can find an SUS for every location of a string of size $n$. Our algorithm significantly improves the $O(
İleri, Atalay Mert +2 more
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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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Suffix-Sorting via Shannon-Fano-Elias Codes
Algorithms, 2010 Given a sequence T = t0t1 . . . tn-1 of size n = |T|, with symbols from a fixed alphabet Σ, (|Σ| ≤ n), the suffix array provides a listing of all the suffixes of T in a lexicographic order.
Donald Adjeroh, Fei Nan
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Efficient Data Structures for Range Shortest Unique Substring Queries
Algorithms, 2020 Let T[1,n] be a string of length n and T[i,j] be the substring of T starting at position i and ending at position j. A substring T[i,j] of T is a repeat if it occurs more than once in T; otherwise, it is a unique substring of T.
Paniz Abedin +3 more
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Privacy-preserving string search on encrypted genomic data using a generalized suffix tree
Informatics in Medicine Unlocked, 2021 Background and objective: Efficient sequencing technologies generate a plethora of genomic data and make it available to researchers. To compute a massive genomic dataset, outsourcing the data to the cloud is often required.
Md Safiur Rahman Mahdi +3 more
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A Gray Box for Visualizing Instruction Sequence Based on Improved Suffix Tree
IEEE Access, 2020 Gray box is a kind of device in which the working process of a program or system is locally recognized. Gray box testing, also known as gray box analysis, is a software debugging method based on the limited cognition of the internal details of the ...
Donglin Wang, Jiandong Fang
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CGAP-align: a high performance DNA short read alignment tool. [PDF]
PLoS ONE, 2013 Next generation sequencing platforms have greatly reduced sequencing costs, leading to the production of unprecedented amounts of sequence data. BWA is one of the most popular alignment tools due to its relatively high accuracy.
Yaoliang Chen +7 more
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