scholarly journals Fast trie-based method for multiple pairwise sequence alignment

2019 ◽  
Vol 484 (4) ◽  
pp. 401-404
Author(s):  
P. A. Yakovlev
Keyword(s):  
Numerical Experiments ◽  
Edit Distance ◽  
Dynamic Programming Algorithm ◽  
Programming Algorithm ◽  
Levenshtein Distance ◽  
Biological Sequences ◽  
Pairwise Sequence Alignment ◽  
Symbol Sequence ◽  
Original Algorithm ◽  
Variable Domains

A method for efficient comparison of a symbol sequence with all strings of a set is presented, which performs considerably faster than the naive enumeration of comparisons with all strings in succession. The procedure is accelerated by applying an original algorithm combining a prefix tree and a standard dynamic programming algorithm searching for the edit distance (Levenshtein distance) between strings. The efficiency of the method is confirmed by numerical experiments with arrays consisting of tens of millions of biological sequences of variable domains of monoclonal antibodies.

scholarly journals Formulation and Analysis of Patterns in a Score Matrix for Global Sequence Alignment

2020 ◽  
Vol 2020 ◽  
pp. 1-9
Author(s):  
James Owusu Asare ◽  
Justice Kwame Appati ◽  
Kwaku Darkwah
Keyword(s):  
Dynamic Programming ◽  
Molecular Biology ◽  
Sequence Alignment ◽  
A Priori ◽  
Dynamic Programming Algorithm ◽  
Evolutionary Relationship ◽  
Programming Algorithm ◽  
Pairwise Sequence Alignment ◽  
Score Matrix ◽  
Unequal Length

Global sequence alignment is one of the most basic pairwise sequence alignment procedures used in molecular biology to understand the similarity that arises among the structure, function, or evolutionary relationship between two nucleotide sequences. The general algorithm associated with global sequence alignment is the dynamic programming algorithm of Needleman and Wunsch. In this paper, patterns are exploited in the score matrix of the Needleman–Wunsch algorithm. With the help of some examples, the general patterns realized are formulated as new a priori propositions and corollaries that are established for both equal and unequal length comparisons of any two arbitrary sequences.

scholarly journals Measurement Aspects of Genome Pattern Investigations - Hardware Implementation

2012 ◽  
Vol 19 (1) ◽  
pp. 49-62
Author(s):  
Andrzej Pułka ◽  
Adam Milik
Keyword(s):  
Dynamic Programming ◽  
Processing Time ◽  
Hardware Implementation ◽  
Dynamic Programming Algorithm ◽  
Programming Algorithm ◽  
Data Path ◽  
Original Algorithm ◽  
A Genome ◽  
Speed Up ◽  
Programmable Devices

Measurement Aspects of Genome Pattern Investigations - Hardware Implementation The work presented in the paper concerns a very important problem of searching for string alignments. The authors show that the problem of a genome pattern alignment could be interpreted and defined as a measuring task, where the distance between two (or more) patterns is investigated. The problem originates from modern computation biology. Hardware-based implementations have been driving out software solutions in the field recently. The complex programmable devices have become very commonly applied. The paper introduces a new, optimized approach based on the Smith-Waterman dynamic programming algorithm. The original algorithm is modified in order to simplify data-path processing and take advantage of the properties offered by FPGA devices. The results obtained with the proposed methodology allow to reduce the size of the functional block and radically speed up the processing time. This approach is very competitive compared with other related works.

scholarly journals Dynamic programming for re-mapping noisy fixations in translation tasks

2013 ◽  
Vol 6 (2) ◽  
Author(s):  
Michael Carl
Keyword(s):  
Dynamic Programming ◽  
Dynamic Programming Algorithm ◽  
Head Movements ◽  
Programming Algorithm ◽  
Second Step ◽  
Symbol Sequence ◽  
Qualitative And Quantitative ◽  
Gaze Patterns ◽  
Symbol Mapping ◽  
Reading Patterns

Eyetrackers which allow for free head movements are in many cases imprecise to the extent that reading patterns become heavily distorted. The poor usability and interpretability of these gaze patterns is corroborated by a "naïve" fixation-to-symbol mapping, which often wrongly maps the possibly drifted center of the observed fixation onto the symbol directly below it. In this paper I extend this naïve fixation-to-symbol mapping by introducing background knowledge about the translation task. In a first step, the sequence of fixation-to-symbol mappings is extended into a lattice of several possible fixated symbols, including those on the line above and below the naïve fixation mapping. In a second step a dynamic programming algorithm applies a number of heuristics to find the best path through the lattice, based on the probable distance in characters, in words and in pixels between successive fixations and the symbol locations, so as to smooth the gazing path according to the background gazing model. A qualitative and quantitative evaluation shows that the algorithm increases the accuracy of the re-mapped symbol sequence.

scholarly journals Efficient computation of spaced seeds

2021 ◽  
Author(s):  
Silvana Ilie
Keyword(s):  
Heuristic Algorithms ◽  
Linear Time ◽  
Dynamic Programming Algorithm ◽  
Hill Climbing ◽  
Programming Algorithm ◽  
Biological Sequences ◽  
Efficient Computation ◽  
Approximate Search ◽  
Spaced Seeds ◽  
Software Programs

Background The most frequently used tools in bioinformatics are those searching for similarities, or local alignments, between biological sequences. Since the exact dynamic programming algorithm is quadratic, linear-time heuristics such as BLAST are used. Spaced seeds are much more sensitive than the consecutive seed of BLAST and using several seeds represents the current state of the art in approximate search for biological sequences. The most important aspect is computing highly sensitive seeds. Since the problem seems hard, heuristic algorithms are used. The leading software in the common Bernoulli model is the SpEED program. Findings SpEED uses a hill climbing method based on the overlap complexity heuristic. We propose a new algorithm for this heuristic that improves its speed by over one order of magnitude. We use the new implementation to compute improved seeds for several software programs. We compute as well multiple seeds of the same weight as MegaBLAST, that greatly improve its sensitivity. Conclusion Multiple spaced seeds are being successfully used in bioinformatics software programs. Enabling researchers to compute very fast high quality seeds will help expanding the range of their applications.

scholarly journals Efficient computation of spaced seeds

2021 ◽  
Author(s):  
Silvana Ilie
Keyword(s):  
Heuristic Algorithms ◽  
Linear Time ◽  
Dynamic Programming Algorithm ◽  
Hill Climbing ◽  
Programming Algorithm ◽  
Biological Sequences ◽  
Efficient Computation ◽  
Approximate Search ◽  
Spaced Seeds ◽  
Software Programs

Background The most frequently used tools in bioinformatics are those searching for similarities, or local alignments, between biological sequences. Since the exact dynamic programming algorithm is quadratic, linear-time heuristics such as BLAST are used. Spaced seeds are much more sensitive than the consecutive seed of BLAST and using several seeds represents the current state of the art in approximate search for biological sequences. The most important aspect is computing highly sensitive seeds. Since the problem seems hard, heuristic algorithms are used. The leading software in the common Bernoulli model is the SpEED program. Findings SpEED uses a hill climbing method based on the overlap complexity heuristic. We propose a new algorithm for this heuristic that improves its speed by over one order of magnitude. We use the new implementation to compute improved seeds for several software programs. We compute as well multiple seeds of the same weight as MegaBLAST, that greatly improve its sensitivity. Conclusion Multiple spaced seeds are being successfully used in bioinformatics software programs. Enabling researchers to compute very fast high quality seeds will help expanding the range of their applications.

Optimization for speed regulation strategy of compound coupled hydro-mechanical transmission

2020 ◽  
pp. 095440702098056
Author(s):  
Jin Yu ◽  
Pengfei Shen ◽  
Zhao Wang ◽  
Yurun Song ◽  
Xiaohan Dong
Keyword(s):  
Fuel Consumption ◽  
Dynamic Programming Algorithm ◽  
Operating Conditions ◽  
Programming Algorithm ◽  
Speed Ratio ◽  
Mechanical Transmission ◽  
Speed Regulation ◽  
Ratio Change ◽  
Low Efficiency ◽  
Wheel Loaders

Heavy duty vehicles, especially special vehicles, including wheel loaders and sprinklers, generally work with drastic changes in load. With the usage of a conventional hydraulic mechanical transmission, they face with these problems such as low efficiency, high fuel consumption and so forth. Some scholars focus on the research to solve these issues. However, few of them take into optimal strategies the fluctuation of speed ratio change, which can also cause a lot of problems. In this study, a novel speed regulation is proposed which cannot only solve problems above but also overcome impact caused by speed ratio change. Initially, based on the former research of the Compound Coupled Hydro-mechanical Transmission (CCHMT), the basic characteristics of CCHMT are analyzed. Besides, to solve these problems, dynamic programming algorithm is utilized to formulate basic speed regulation strategy under specific operating condition. In order to reduce the problem caused by speed ratio change, a new optimization is applied. The results indicate that the proposed DP optimal speed regulation strategy has better performance on reducing fuel consumption by up to 1.16% and 6.66% in driving cycle JN1015 and in ECE R15 working condition individually, as well as smoothing the fluctuation of speed ratio by up to 12.65% and 19.01% in those two driving cycles respectively. The processes determining the speed regulation strategy can provide a new method to formulate the control strategies of CCHMT under different operating conditions particularlly under real-world conditions.

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