Notice of Retraction: Similarity Analysis of DNA Sequences Based on LZ Complexity and Dynamic Programming Algorithm

2011 ◽  
Author(s):  
Xiaodong Guo ◽  
Qi Dai ◽  
Bin Han ◽  
Lei Zhu ◽  
Lihua Li
Keyword(s):  
Dynamic Programming ◽  
Dna Sequences ◽  
Dynamic Programming Algorithm ◽  
Programming Algorithm ◽  
Similarity Analysis ◽  
Lz Complexity

REDUCING THE SEARCH SPACE AND TIME COMPLEXITY OF NEEDLEMAN-WUNSCH ALGORITHM (GLOBAL ALIGNMENT) AND SMITH-WATERMAN ALGORITHM (LOCAL ALIGNMENT) FOR DNA SEQUENCE ALIGNMENT

2015 ◽  
Vol 77 (20) ◽  
Author(s):  
F. N. Muhamad ◽  
R. B. Ahmad ◽  
S. Mohd. Asi ◽  
M. N. Murad
Keyword(s):  
Dynamic Programming ◽  
Dna Sequences ◽  
Sequence Comparison ◽  
Dynamic Programming Algorithm ◽  
Search Space ◽  
Programming Algorithm ◽  
Local Alignment ◽  
Global Alignment ◽  
Main Research ◽  
Dna Sequence Alignment

The fundamental procedure of analyzing sequence content is sequence comparison. Sequence comparison can be defined as the problem of finding which parts of the sequences are similar and which parts are different, namely comparing two sequences to identify similarities and differences between them. A typical approach to solve this problem is to find a good and reasonable alignment between the two sequences. The main research in this project is to align the DNA sequences by using the Needleman-Wunsch algorithm for global alignment and Smith-Waterman algorithm for local alignment based on the Dynamic Programming algorithm. The Dynamic Programming Algorithm is guaranteed to find optimal alignment by exploring all possible alignments and choosing the best through the scoring and traceback techniques. The algorithms proposed and evaluated are to reduce the gaps in aligning sequences as well as the length of the sequences aligned without compromising the quality or correctness of results. In order to verify the accuracy and consistency of measurements obtained in Needleman-Wunsch and Smith-Waterman algorithms the data is compared with Emboss (global) and Emboss (local) with 600 strands test data.

A BIT-PARALLEL DYNAMIC PROGRAMMING ALGORITHM SUITABLE FOR DNA SEQUENCE ALIGNMENT

2012 ◽  
Vol 10 (04) ◽  
pp. 1250002 ◽  
Author(s):  
KOUICHI KIMURA ◽  
ASAKO KOIKE ◽  
KENTA NAKAI
Keyword(s):  
Dynamic Programming ◽  
Dna Sequences ◽  
Time Complexity ◽  
Reference Genome ◽  
Dynamic Programming Algorithm ◽  
Programming Algorithm ◽  
Short Read ◽  
Word Size ◽  
Dna Sequence Alignment ◽  
Query Length

Myers' elegant and powerful bit-parallel dynamic programming algorithm for approximate string matching has a restriction that the query length should be within the word size of the computer, typically 64. We propose a modification of Myers' algorithm, in which the modification has a restriction not on the query length but on the maximum number of mismatches (substitutions, insertions, or deletions), which should be less than half of the word size. The time complexity is O(m log |Σ|), where m is the query length and |Σ| is the size of the alphabet Σ. Thus, it is particularly suited for sequences on a small alphabet such as DNA sequences. In particular, it is useful in quickly extending a large number of seed alignments against a reference genome for high-throughput short-read data produced by next-generation DNA sequencers.

Optimization in Trajectory Planning of Multi-Jointed Fingers in Dextrous Hand Designs

1991 ◽  
Author(s):  
A. Meghdari ◽  
H. Sayyaadi
Keyword(s):  
Dynamic Programming ◽  
Motion Control ◽  
Trajectory Planning ◽  
Degrees Of Freedom ◽  
Optimization Technique ◽  
Dynamic Programming Algorithm ◽  
Programming Algorithm ◽  
Kinematics And Dynamics ◽  
Feasible Solutions ◽  
Dextrous Hand

Abstract An optimization technique based on the well known Dynamic Programming Algorithm is applied to the motion control trajectories and path planning of multi-jointed fingers in dextrous hand designs. A three fingered hand with each finger containing four degrees of freedom is considered for analysis. After generating the kinematics and dynamics equations of such a hand, optimum values of the joints torques and velocities are computed such that the finger-tips of the hand are moved through their prescribed trajectories with the least time or/and energy to reach the object being grasped. Finally, optimal as well as feasible solutions for the multi-jointed fingers are identified and the results are presented.

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