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Dynamic extended suffix arrays

M. Salson, T. Lecroq, M. Léonard, L. Mouchard
2010 Journal of Discrete Algorithms  
We furthermore explain how this technique can be adapted for maintaining a sample of the Extended Suffix Array, containing a sample of the Suffix Array, a sample of the Inverse Suffix Array and the whole  ...  This algorithm is based on a recent four-stage algorithm developed for dynamic Burrows-Wheeler Transforms (BWT).  ...  The Extended Suffix Array ESA, containing both SA and LCP , can easily replace the standard suffix tree.  ... 
doi:10.1016/j.jda.2009.02.007 fatcat:3rwijo4skraghjcclg3eyurkwq

A Modification of the Landau-Vishkin Algorithm Computing Longest Common Extensions via Suffix Arrays [chapter]

Rodrigo de Castro Miranda, Mauricio Ayala-Rincón
2005 Lecture Notes in Computer Science  
We present a variation of the Landau-Vishkin algorithm which instead of suffix trees uses suffix arrays for computing the longest common extensions, thereby improving actual space usage.  ...  Landau and Vishkin developed an algorithm which uses suffix trees for accelerating the computation along the dynamic programming table and reaching space and running time in O(nk), where n > m and k is  ...  We have shown that it is possible to change the Landau-Vishkin approximate string matching algorithm to use enhanced suffix arrays instead of suffix trees for its computation of longest common extensions  ... 
doi:10.1007/11532323_25 fatcat:dyplnkcednbohfqttzzdwmqfe4

Dynamic Suffix Array with Sub-linear update time and Poly-logarithmic Lookup Time [article]

Amihood Amir, Itai Boneh
2021 arXiv   pre-print
The Suffix Array SA_S[1... n] of an n-length string S is a lexicographically sorted array of the suffixes of S.  ...  We present a data structure for maintaining a representation of the suffix array of a dynamic string which undergoes symbol substitutions, deletions, and insertions.  ...  Dynamic Suffix Array As in our solution for inverse suffix arrays, we build upon the data structure presented in [4] .  ... 
arXiv:2112.12678v1 fatcat:vyhkhb4iafak7egvs6clpbapte

Searching Gapped Palindromes in DNA Sequences using Dynamic Suffix Array

Shivika Gupta, Rajesh Prasad, Sunita Yadav
2015 Indian Journal of Science and Technology  
The concept of Dynamic Suffix Array (DSA) is used to propose algorithms to search two classes of gapped palindromes-length constrained and long armed.  ...  DSA modifies the previous built suffix arrays when there is insertion and deletion of a new character, due to which efficiency is improved.  ...  DSA is based on the dynamic construction of new suffix array 5 from the previously built suffix arrays.  ... 
doi:10.17485/ijst/2015/v8i23/70645 fatcat:lyma3zepv5fldpbkh3bfysofau

Inexact Local Alignment Search over Suffix Arrays

Mohammadreza Ghodsi, Mihai Pop
2009 2009 IEEE International Conference on Bioinformatics and Biomedicine  
We show how to adapt this algorithm to work over the memory efficient suffix array with provably minimal overhead in running time.  ...  Space requirements of suffix arrays can be further reduced to O(n) bits using compressed suffix arrays.  ...  element of suffix array, then for every k ∈ [i . . . j], every suffix pointed to by the kth element of suffix array shares the same prefix.  ... 
doi:10.1109/bibm.2009.25 pmid:21278916 pmcid:PMC3029072 dblp:conf/bibm/GhodsiP09 fatcat:vw5gcpdpuvfubd4dnclskxnljq

Variations of the parameterized longest previous factor

Richard Beal, Donald Adjeroh
2012 Journal of Discrete Algorithms  
We show in [10] that the pLPF problem is not a straightforward extension of the LPF problem because of the added challenges of the p-match and dynamic nature of the parameterized suffixes (p-suffixes)  ...  The following theorems formalize our core contributions, where pSA S denotes the p-suffix array on p-string S. Theorem 16.  ...  As a result, Lemma 15 permits us to adapt the basic algorithm compute_LPF given in [15] for our pLPF problem by extending the solution to incorporate the dynamic matching of p-suffixes.  ... 
doi:10.1016/j.jda.2012.05.004 fatcat:sp34gq4frneflegjscyrlwjvae

Engineering Small Space Dictionary Matching [article]

Shoshana Marcus Dina Sokol
2013 arXiv   pre-print
We use the compressed suffix tree as the underlying data structure of our algorithm, thus, the working space of our algorithm is proportional to the optimal compression of the dictionary.  ...  Extending this work to the dynamic setting would begin by implementing the dynamic compressed suffix tree to accommodate insertion, deletion, and modification of dictionary patterns, without rebuilding  ...  Their algorithm uses the compressed suffix tree of Sadakane [21] , which they extended so that it can support a dynamically changing dictionary of patterns.  ... 
arXiv:1301.6428v1 fatcat:5k34y7ew2jb5fbgvpu2xj7snn4

Extended suffix array construction using Lyndon factors

Sunita, Deepak Garg
2018 Sadhana (Bangalore)  
In this paper, we are extending the novel approach of incremental suffix array construction using Lyndon factorization to the construction of extended suffix array where extended suffix array is the suffix  ...  Main motive behind the incremental and simultaneous construction of suffix array and LCP array is that both involve in calculating the order information by considering the common prefixes of the suffixes  ...  and extended suffix array.  ... 
doi:10.1007/s12046-018-0832-z fatcat:nguhgupnpzh2dbfqdl2uqhvbfy

Cross-Document Pattern Matching [chapter]

Gregory Kucherov, Yakov Nekrich, Tatiana Starikovskaya
2012 Lecture Notes in Computer Science  
Since the suffix array is not well-suited for dynamic updates, at Step 1 we will use the generalized suffix tree for T 1 , T 2 , . . . , T m hereafter denoted GST .  ...  For each considered suffix array, we assume available, when needed, two auxiliary arrays: an inverted suffix array and another array, called the LCP-array, of longest common prefixes between each suffix  ... 
doi:10.1007/978-3-642-31265-6_16 fatcat:hb2njzigavao3eo6q4n6grjmzy

Indexing huge genome sequences for solving various problems

K Sadakane, T Shibuya
2001 Genome Informatics Series  
Suffix trees and suffix arrays are used for simple queries.  ...  We use the compressed suffix array. It compactly stores the suffix array at the cost of theoretically a small slowdown in access speed.  ...  Compressed Suffix Arrays The compressed suffix array is a compressed version of the suffix array.  ... 
pmid:11791236 fatcat:5vhtru6hnvhtjlfuytzxwt34ta

A Practical Semi-External Memory Method for Approximate Pattern Matching

Daniel Saad Nogueira Nunes, Mauricio Ayala-Rincón
2016 Electronical Notes in Theoretical Computer Science  
However, the amount of available memory limits the usage of their algorithm, since it requires all the answer array be in memory.  ...  This algorithm is based on a dynamic programming technique which, at the k th iteration, obtains the maximal extension of diagonals of the dynamic programming table Table 1 Suffix array for T = T #P  ...  It uses directcomparisons only if the distance in the Suffix Array from the suffixes P L[i]+1 and T i+L[i]+1 is large enough (suffixes which are close in the Suffix Array tend to share more symbols).  ... 
doi:10.1016/j.entcs.2016.09.010 fatcat:nvtyexzbafg63iehsnjqk5gq5q

GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array

Shuji Suzuki, Masanori Kakuta, Takashi Ishida, Yutaka Akiyama, Ahmed Moustafa
2014 PLoS ONE  
We designed a new homology search algorithm that finds seed sequences based on the suffix arrays of a query and a database, and have implemented it as GHOSTX.  ...  Suffix Array Seed Search For two suffix arrays, we can find all the local matches using dynamic programming [10] .  ...  The suffix array of T is SA, that is, an array of pointers to all the suffixes of T in lexicographical order.  ... 
doi:10.1371/journal.pone.0103833 pmid:25099887 pmcid:PMC4123905 fatcat:gbu4bx2cdjdchdj7rjkysokkfu

Indexing Huge Genome Sequences for Solving Various Problems

Kunihiko Sadakane, Tetsuo Shibuya
2001 Genome Informatics Series  
Suffix trees and suffix arrays are used for simple queries.  ...  We use the compressed suffix array. It compactly stores the suffix array at the cost of theoretically a small slowdown in access speed.  ...  Compressed Suffix Arrays The compressed suffix array is a compressed version of the suffix array.  ... 
doi:10.11234/gi1990.12.175 fatcat:gkz6c2cfqvcyfjiebgyawfrpqu

Parameterized longest previous factor

Richard Beal, Donald Adjeroh
2012 Theoretical Computer Science  
The major difficulty of the pLPF problem is that unlike traditional suffixes of a string, the p-suffixes are dynamic, varying with the starting position of the p-suffix.  ...  Our approach uses a parameterized suffix array (pSA) [10-13] for p-strings analogous to the traditional suffix array [14] .  ...  In general, we handle the dynamically changing p-suffixes differently than P-Kasai to save space and we use extra space to retain previous matches in order to more quickly extend future matches.  ... 
doi:10.1016/j.tcs.2012.02.004 fatcat:anybcnp34bb6volch62kvbw46u

Engineering a compressed suffix tree implementation

N. Välimäki, V. Mäkinen, W. Gerlach, K. Dixit
2009 ACM Journal of Experimental Algorithmics  
Our experiments show that, e.g. on a 10 MB DNA sequence, the compressed suffix tree takes 10% of the space of normal suffix tree.  ...  The compressed suffix tree occupies space proportional to the text size, i.e. O(n log |Σ|) bits, and supports all typical suffix tree operations with at most log n factor slowdown.  ...  Very recently Sadakane [25] extended the abstract data structure concept to cover suffix trees, identifying typical operations suffix trees are assumed to possess.  ... 
doi:10.1145/1498698.1594228 fatcat:7lbrz6keync55ic54a35cha6uq
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