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Simple and flexible detection of contiguous repeats using a suffix tree [PDF]
, 2002 Stoye J, Gusfield D. Simple and flexible detection of contiguous repeats using a suffix tree. Theoretical Computer Science. 2002;270(1-2):843-856.We study the problem of detecting all occurrences of (primitive) tandem repeats and tandem arrays in a ...
Jens Stoye +4 more
core +2 more sources
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
doaj +1 more source
PFP Compressed Suffix Trees [PDF]
, 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
openaire +3 more sources
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
doaj +1 more source
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
doaj +1 more source
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
doaj +1 more source
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
doaj +1 more source
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
doaj +1 more source
INVESTIGAÇÃO HISTÓRICA DO SUFIXO –“EIR”- NA NOMEAÇÃO DE VEGETAIS EM LÍNGUA PORTUGUESA
Studia Universitatis Babeş-Bolyai. Philologia, 2021 A Historical Investigation of the Suffix -eir- for the Naming of Plants in the Portuguese Language. The Latin suffix -ari-, used as a creator of adjectives, developed several meanings during the period of spoken late Latin, as well as in the formation ...
Natival SIMÕES NETO +1 more
doaj +1 more source