A copy of this work was available on the public web and has been preserved in the Wayback Machine. The capture dates from 2012; you can also visit the original URL.
The file type is `application/pdf`

.

## Filters

##
###
Dynamic extended suffix arrays

2010
*
Journal of Discrete Algorithms
*

We furthermore explain how this technique can be adapted for maintaining a sample of the

doi:10.1016/j.jda.2009.02.007
fatcat:3rwijo4skraghjcclg3eyurkwq
*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. ...##
###
A Modification of the Landau-Vishkin Algorithm Computing Longest Common Extensions via Suffix Arrays
[chapter]

2005
*
Lecture Notes in Computer Science
*

We present a variation of the Landau-Vishkin algorithm which instead of

doi:10.1007/11532323_25
fatcat:dyplnkcednbohfqttzzdwmqfe4
*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 ...##
###
Dynamic Suffix Array with Sub-linear update time and Poly-logarithmic Lookup Time
[article]

2021
*
arXiv
*
pre-print

The

arXiv:2112.12678v1
fatcat:vyhkhb4iafak7egvs6clpbapte
*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] . ...##
###
Searching Gapped Palindromes in DNA Sequences using Dynamic Suffix Array

2015
*
Indian Journal of Science and Technology
*

The concept of

doi:10.17485/ijst/2015/v8i23/70645
fatcat:lyma3zepv5fldpbkh3bfysofau
*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*. ...##
###
Inexact Local Alignment Search over Suffix Arrays

2009
*
2009 IEEE International Conference on Bioinformatics and Biomedicine
*

We show how to adapt this algorithm to work over the memory efficient

doi:10.1109/bibm.2009.25
pmid:21278916
pmcid:PMC3029072
dblp:conf/bibm/GhodsiP09
fatcat:vw5gcpdpuvfubd4dnclskxnljq
*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. ...##
###
Variations of the parameterized longest previous factor

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

doi:10.1016/j.jda.2012.05.004
fatcat:sp34gq4frneflegjscyrlwjvae
*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*. ...##
###
Engineering Small Space Dictionary Matching
[article]

2013
*
arXiv
*
pre-print

We use the compressed

arXiv:1301.6428v1
fatcat:5k34y7ew2jb5fbgvpu2xj7snn4
*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. ...##
###
Extended suffix array construction using Lyndon factors

2018
*
Sadhana (Bangalore)
*

In this paper, we are

doi:10.1007/s12046-018-0832-z
fatcat:nguhgupnpzh2dbfqdl2uqhvbfy
*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*. ...##
###
Cross-Document Pattern Matching
[chapter]

2012
*
Lecture Notes in Computer Science
*

Since the

doi:10.1007/978-3-642-31265-6_16
fatcat:hb2njzigavao3eo6q4n6grjmzy
*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*...##
###
Indexing huge genome sequences for solving various problems

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*. ...

##
###
A Practical Semi-External Memory Method for Approximate Pattern Matching

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

doi:10.1016/j.entcs.2016.09.010
fatcat:nvtyexzbafg63iehsnjqk5gq5q
*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). ...##
###
GHOSTX: An Improved Sequence Homology Search Algorithm Using a Query Suffix Array and a Database Suffix Array

2014
*
PLoS ONE
*

We designed a new homology search algorithm that finds seed sequences based on the

doi:10.1371/journal.pone.0103833
pmid:25099887
pmcid:PMC4123905
fatcat:gbu4bx2cdjdchdj7rjkysokkfu
*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. ...##
###
Indexing Huge Genome Sequences for Solving Various Problems

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*. ...

##
###
Parameterized longest previous factor

2012
*
Theoretical Computer Science
*

The major difficulty of the pLPF problem is that unlike traditional

doi:10.1016/j.tcs.2012.02.004
fatcat:anybcnp34bb6volch62kvbw46u
*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. ...##
###
Engineering a compressed suffix tree implementation

2009
*
ACM Journal of Experimental Algorithmics
*

Our experiments show that, e.g. on a 10 MB DNA sequence, the compressed

doi:10.1145/1498698.1594228
fatcat:7lbrz6keync55ic54a35cha6uq
*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. ...
« Previous

*Showing results 1 — 15 out of 10,290 results*