Near-optimal block alignments

被引：1

作者：

Tseng, Kuo-Tsung ^{[1
]}

Yang, Chang-Biau ^{[1
]}

Huang, Kuo-Si ^{[1
]}

Peng, Yung-Hsing ^{[1
]}

机构：

[1] Natl Sun Yat Sen Univ, Dept Comp Sci & Engn, Kaohsiung 80424, Taiwan

来源：

IEICE TRANSACTIONS ON INFORMATION AND SYSTEMS | 2008年 / E91D卷 / 03期

关键词：

computational biology; longest common subsequence; biosequence alignment; near-optimal alignments;

D O I：

10.1093/ietisy/e91-d.3.789

中图分类号：

TP [自动化技术、计算机技术];

学科分类号：

0812 ;

摘要：

The optimal alignment of two given biosequences is mathematically optimal, but it may not be a biologically optimal one. To investigate more possible alignments with biological meaning, one can relax the scoring functions to get near-optimal alignments. Though the near optimal alignments increase the possibility of finding the correct alignment, they may confuse the biologists because the size of candidates is large. In this paper, we present the filter scheme for the near-optimal alignments. An easy method for tracing the near-optimal alignments and an algorithm for filtering those alignments are proposed. The time complexity of our algorithm is 0(dmn) in the worst case, where d is the maximum distance between the near-optimal alignments and the optimal alignment, and m and n are the lengths of the input sequences, respectively.

引用

页码：789 / 795

页数：7

共 50 条

[11] Universal near-optimal feedbacks
Nobakhtian, S
Stern, RJ
JOURNAL OF OPTIMIZATION THEORY AND APPLICATIONS, 2000, 107 (01) : 89 - 122
[12] NEAR-OPTIMAL DECODING ALGORITHM
KOROGODI.AM
TELECOMMUNICATIONS AND RADIO ENGINEERING, 1972, 26 (09) : 130 - 132
[13] THE NEAR-OPTIMAL INSTRUCTION SET
SMITH, T
IEEE MICRO, 1982, 2 (03) : 5 - 6
[14] Distributed near-optimal matching
Deng, XT
COMBINATORICA, 1996, 16 (04) : 453 - 464
[15] Efficient Near-Optimal Testing of Community Changes in Balanced Stochastic Block Models
Gangrade, Aditya
Venkatesh, Praveen
Nazer, Bobak
Saligrama, Venkatesh
ADVANCES IN NEURAL INFORMATION PROCESSING SYSTEMS 32 (NIPS 2019), 2019, 32
[16] Near-Optimal Online Auctions
Blum, Avrim
Hartline, Jason D.
PROCEEDINGS OF THE SIXTEENTH ANNUAL ACM-SIAM SYMPOSIUM ON DISCRETE ALGORITHMS, 2005, : 1156 - 1163
[17] Near-optimal terrain collision
Malaek, S. M.
Abbasi, A.
2006 IEEE AEROSPACE CONFERENCE, VOLS 1-9, 2006, : 2990 - +
[18] Near-optimal adaptive polygonization
Seibold, W
Joy, KI
COMPUTER GRAPHICS INTERNATIONAL, PROCEEDINGS, 1999, : 206 - 213
[19] Near-Optimal Light Spanners
Chechik, Shiri
Wulff-Nilsen, Christian
ACM TRANSACTIONS ON ALGORITHMS, 2018, 14 (03)
[20] Near-optimal list colorings
Molloy, M
Reed, B
RANDOM STRUCTURES & ALGORITHMS, 2000, 17 (3-4) : 376 - 402

← 1 2 3 4 5 →