作者: 苦笑 時(shí)間: 2025-3-21 22:47
An Extension of the Burrows Wheeler Transform and Applications to Sequence Comparison and Data Comp ., is reversible, but, differently from ., it is also surjective. The . transformation allows to give a definition of distance between two sequences, that we apply here to the problem of the whole mitochondrial genome phylogeny. Moreover we give some consideration about compressing a set of words by using the . transformation as preprocessing.作者: 摻假 時(shí)間: 2025-3-22 01:58 作者: Aromatic 時(shí)間: 2025-3-22 05:47
Lecture Notes in Electrical EngineeringWe present a new simple algorithm that constructs an Aho Corasick automaton for a set of patterns, ., of total length ., in .(.) time and space for integer alphabets. Processing a text of size . over an alphabet Σ with the automaton costs ., where there are . occurrences of patterns in the text.作者: BILK 時(shí)間: 2025-3-22 10:54
Construction of Aho Corasick Automaton in Linear Time for Integer Alphabets,We present a new simple algorithm that constructs an Aho Corasick automaton for a set of patterns, ., of total length ., in .(.) time and space for integer alphabets. Processing a text of size . over an alphabet Σ with the automaton costs ., where there are . occurrences of patterns in the text.作者: 收集 時(shí)間: 2025-3-22 13:29 作者: 收集 時(shí)間: 2025-3-22 18:23
Smart Grid and Internet of Things two problem have been studied extensively. The former was previously proved to be not polynomial-time approximable within ratio . . for a constant .. The latter was previously proved to be .-hard and have a PTAS. In this paper, the longest common rigid subsequence problem (LCRS) is studied. LCRS sh作者: 泥沼 時(shí)間: 2025-3-23 00:20
https://doi.org/10.1007/978-3-031-20398-5ccurrences of a pattern when allowing a constant number of errors. In particular, our index can be built to report all occurrences, all positions, or all documents where a pattern occurs in time linear in the size of the query string and the number of results. This improves over previous work where 作者: Additive 時(shí)間: 2025-3-23 03:57 作者: 無節(jié)奏 時(shí)間: 2025-3-23 05:46
Shasha Zhang,Haiyan Kang,Dong Yud text), permits efficient search for the occurrences of a pattern .=. . . .... . . in ., and is able to reproduce any text substring, so the self-index replaces the text. Several remarkable self-indexes have been developed in recent years. They usually take .(. .) or .(. .) bits, being . . the .th 作者: Lipohypertrophy 時(shí)間: 2025-3-23 11:04 作者: Infraction 時(shí)間: 2025-3-23 17:45 作者: 綁架 時(shí)間: 2025-3-23 19:32
Haiyan Kang,Yaping Feng,Xiameng Siations including text processing and DNA sequence analysis. In this paper, we present a fast algorithm for approximate string matching, called FAAST. It aims at solving a popular variant of the approximate string matching problem, the ., whose objective is to find all occurrences of a short pattern 作者: 離開真充足 時(shí)間: 2025-3-23 23:13 作者: Assault 時(shí)間: 2025-3-24 02:32
Xiaoying Qiu,Xuan Sun,Xiameng Siondensed neighborhoods are not a minimal representation of a pattern neighborhood. We show that we can restrict our attention to super condensed neighborhoods which are minimal. We then present an algorithm for generating Super Condensed Neighborhoods. The algorithm runs in .(.? . / . ? .), where . 作者: nonradioactive 時(shí)間: 2025-3-24 06:43 作者: STRIA 時(shí)間: 2025-3-24 13:20
https://doi.org/10.1007/978-3-030-49610-4attern was introduced in?[12]. In this paper, we present a new tool for representation and detection of gene clusters in multiple genomes, using PQ trees?[6]: this describes the inner structure and the relations between clusters succinctly, aids in filtering meaningful from apparently meaningless cl作者: 徹底明白 時(shí)間: 2025-3-24 18:24
Yulin Duan,Dandan Li,Chongke Biation algorithms, in which text regions dissimilar to the pattern are excluded (filtered out) in a first step, and remaining regions are compared to the pattern by dynamic programming in a second step. Among the necessary conditions used to test similarity between the regions and the pattern, many r作者: EXCEL 時(shí)間: 2025-3-24 19:28 作者: 爭吵加 時(shí)間: 2025-3-24 23:46
Smart Grid and Renewable Energy Systems ., is reversible, but, differently from ., it is also surjective. The . transformation allows to give a definition of distance between two sequences, that we apply here to the problem of the whole mitochondrial genome phylogeny. Moreover we give some consideration about compressing a set of words b作者: Allodynia 時(shí)間: 2025-3-25 03:31 作者: prediabetes 時(shí)間: 2025-3-25 10:39 作者: 陳腐的人 時(shí)間: 2025-3-25 12:05 作者: Redundant 時(shí)間: 2025-3-25 19:18 作者: dyspareunia 時(shí)間: 2025-3-25 21:09
0302-9743 Overview: Includes supplementary material: 978-3-540-26201-5978-3-540-31562-9Series ISSN 0302-9743 Series E-ISSN 1611-3349 作者: 虛假 時(shí)間: 2025-3-26 03:43
https://doi.org/10.1007/978-3-030-49610-4t they may accept infinite strings. But by assigning weights to the edges, the acceptable strings are limited only to the substrings of input strings. The size of WDWGs is smaller than that of DAWGs both in theory and practice. A linear-time on-line construction algorithm for WDWGs is also presented.作者: 疲憊的老馬 時(shí)間: 2025-3-26 05:12 作者: CUB 時(shí)間: 2025-3-26 10:03 作者: 惰性女人 時(shí)間: 2025-3-26 15:40
Alberto Apostolico,Maxime Crochemore,Kunsoo ParkIncludes supplementary material: 作者: 時(shí)代錯(cuò)誤 時(shí)間: 2025-3-26 16:56 作者: 藥物 時(shí)間: 2025-3-26 23:11 作者: 條街道往前推 時(shí)間: 2025-3-27 03:53 作者: 經(jīng)典 時(shí)間: 2025-3-27 06:17 作者: enchant 時(shí)間: 2025-3-27 10:02
https://doi.org/10.1007/978-3-031-20398-5input size . and queries with up to . errors. Additionally, we present a trade-off between query time and index complexity that achieves worst-case bounded index size and preprocessing time with linear lookup time on average.作者: PAN 時(shí)間: 2025-3-27 16:28
Sai Liu,Zhen-Jiang Zhang,Yong Cui,Yang Zhang . substring of text starting at . is not greater than ., i.e. ...We provide an algorithm that solves the .-. .-distance problem in time .. The algorithm applies a bounded divide-and-conquer approach and makes novel uses of non-boolean convolutions.作者: fringe 時(shí)間: 2025-3-27 20:51
Xiaoying Qiu,Xuan Sun,Xiameng Sitime, where . is the size of the condensed neighborhood. We further improve this algorithm by using Bit-Parallelism and Increased Bit-Parallelism techniques. Our experimental results show that the resulting algorithm is very fast.作者: Radiation 時(shí)間: 2025-3-27 23:34 作者: intercede 時(shí)間: 2025-3-28 04:03 作者: Ventricle 時(shí)間: 2025-3-28 07:49 作者: fatty-acids 時(shí)間: 2025-3-28 11:21
An Efficient Algorithm for Generating Super Condensed Neighborhoods,time, where . is the size of the condensed neighborhood. We further improve this algorithm by using Bit-Parallelism and Increased Bit-Parallelism techniques. Our experimental results show that the resulting algorithm is very fast.作者: PSA-velocity 時(shí)間: 2025-3-28 15:00 作者: 犬儒主義者 時(shí)間: 2025-3-28 20:21 作者: CLAM 時(shí)間: 2025-3-28 22:56
On the Longest Common Rigid Subsequence Problem,ares similarity with LCS and CSP and has an important application in motif finding in biological sequences. LCRS is proved to be . hard in this paper. An exact algorithm with quasi-polynomial average running time is also provided.作者: 冷峻 時(shí)間: 2025-3-29 05:37
Linear-Time Construction of Compressed Suffix Arrays Using ,(, log ,)-Bit Working Space for Large A construct the index data structures for large alphabets. Our algorithm constructs the suffix array, the CSA, and the FM-index using .(.) time and .-bit working space, where . = log. 2. Our algorithm takes less time and more space than Hon et al.’s algorithm. Our algorithm uses least working space among alphabet-independent linear-time algorithms.作者: deciduous 時(shí)間: 2025-3-29 11:01
On the Complexity of Sparse Exon Assembly,described in [5] yields an .(. .) result for spliced alignment, regardless of filtration mode..In this paper we suggest a new algorithm which targets the case where filtering has been applied to the data, resulting in a set of .(.) candidate exon blocks. Our algorithm yields an . solution for this case.作者: 狂熱語言 時(shí)間: 2025-3-29 11:34 作者: ELATE 時(shí)間: 2025-3-29 17:40
Cheng-fan Li,Jia-xin Huang,Shao-chun Wuare centered around the origin or the terminus of replication [8,10,18]. This constraint simplifies the median problem significantly. More precisely, we show that the median problem for the reversal distance can be solved in linear time for circular bacterial genomes.作者: MAIM 時(shí)間: 2025-3-29 21:56 作者: 不適當(dāng) 時(shí)間: 2025-3-30 01:56 作者: 共同給與 時(shí)間: 2025-3-30 08:00
Smart Grid and Internet of Thingsares similarity with LCS and CSP and has an important application in motif finding in biological sequences. LCRS is proved to be . hard in this paper. An exact algorithm with quasi-polynomial average running time is also provided.作者: corn732 時(shí)間: 2025-3-30 09:00 作者: 名次后綴 時(shí)間: 2025-3-30 13:41
Lecture Notes in Electrical Engineeringdescribed in [5] yields an .(. .) result for spliced alignment, regardless of filtration mode..In this paper we suggest a new algorithm which targets the case where filtering has been applied to the data, resulting in a set of .(.) candidate exon blocks. Our algorithm yields an . solution for this case.作者: Clinch 時(shí)間: 2025-3-30 17:26
Sharper Upper and Lower Bounds for an Approximation Scheme for , ,problem is an abstraction of motif finding, a common bioinformatics discovery task. The PTAS due to Li . is simple, and a preliminary implementation [8] gave reasonable results in practice. However, the previously known bounds on its performance are useless when runtimes are actually manageable. Her作者: 樣式 時(shí)間: 2025-3-30 22:07 作者: 突變 時(shí)間: 2025-3-31 04:28 作者: liposuction 時(shí)間: 2025-3-31 06:26 作者: 帽子 時(shí)間: 2025-3-31 12:03
Succinct Suffix Arrays Based on Run-Length Encoding,d text), permits efficient search for the occurrences of a pattern .=. . . .... . . in ., and is able to reproduce any text substring, so the self-index replaces the text. Several remarkable self-indexes have been developed in recent years. They usually take .(. .) or .(. .) bits, being . . the .th 作者: 使隔離 時(shí)間: 2025-3-31 15:59
Linear-Time Construction of Compressed Suffix Arrays Using ,(, log ,)-Bit Working Space for Large Aor constructing these index data structures have been developed. Recently, Hon et al. [11] proposed a construction algorithm using .(. ·loglog|Σ|) time and .(.log|Σ|)-bit working space, which is the fastest algorithm using .(.log|Σ|)-bit working space..In this paper we give an efficient algorithm to作者: 痛恨 時(shí)間: 2025-3-31 19:12
Faster Algorithms for ,,,-Matching and Related Problems,ms is shown to be .(. log .), where . is the pattern length, . is the text length and . a given integer. Our approach makes use of Fourier transform methods and the running times are independent of the alphabet size. . algorithms for the .-matching and total-difference problems are also given. In al作者: opinionated 時(shí)間: 2025-3-31 23:54
A Fast Algorithm for Approximate String Matching on Gene Sequences,ations including text processing and DNA sequence analysis. In this paper, we present a fast algorithm for approximate string matching, called FAAST. It aims at solving a popular variant of the approximate string matching problem, the ., whose objective is to find all occurrences of a short pattern 作者: 搖晃 時(shí)間: 2025-4-1 04:50 作者: 倔強(qiáng)一點(diǎn) 時(shí)間: 2025-4-1 09:20
An Efficient Algorithm for Generating Super Condensed Neighborhoods,ondensed neighborhoods are not a minimal representation of a pattern neighborhood. We show that we can restrict our attention to super condensed neighborhoods which are minimal. We then present an algorithm for generating Super Condensed Neighborhoods. The algorithm runs in .(.? . / . ? .), where . 作者: Gossamer 時(shí)間: 2025-4-1 10:52 作者: 乳汁 時(shí)間: 2025-4-1 15:02
Using PQ Trees for Comparative Genomics,attern was introduced in?[12]. In this paper, we present a new tool for representation and detection of gene clusters in multiple genomes, using PQ trees?[6]: this describes the inner structure and the relations between clusters succinctly, aids in filtering meaningful from apparently meaningless cl作者: 首創(chuàng)精神 時(shí)間: 2025-4-1 19:15
Hardness of Optimal Spaced Seed Design,ation algorithms, in which text regions dissimilar to the pattern are excluded (filtered out) in a first step, and remaining regions are compared to the pattern by dynamic programming in a second step. Among the necessary conditions used to test similarity between the regions and the pattern, many r作者: 合并 時(shí)間: 2025-4-2 00:55 作者: Myofibrils 時(shí)間: 2025-4-2 03:56 作者: Occupation 時(shí)間: 2025-4-2 10:45 作者: 玉米 時(shí)間: 2025-4-2 13:00
On the Complexity of Sparse Exon Assembly,, was introduced by Gelfand, Mironov and Pevzner [5]. The method works by finding a set of blocks in a source genomic sequence . whose concatenation (splicing) fits a target gene . belonging to a homologous species. Let .,. and the candidate exons be sequences of size .(.). The innovative algorithm 作者: misshapen 時(shí)間: 2025-4-2 19:16
An Upper Bound on the Hardness of Exact Matrix Based Motif Discovery,l known as a score matrix. Matrix based motif discovery has been extensively studied but no positive results have been known regarding its theoretical hardness. We present the first non-trivial upper bound on the complexity (worst-case computation time) of this problem. Other than linear terms, our
