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A Method for Multiple Sequence Alignment Based on Particle Swarm Optimization [chapter]

Fasheng Xu, Yuehui Chen
2009 Lecture Notes in Computer Science  
Sequence Alignment is a basic information disposal method in Bioinformatics. However, it is difficult to deal with multiple sequence alignment problem(MSA).  ...  In the algorithm, each particle represents an alignment and flies to the particle which has the best solution by some rules.  ...  behavior of large animal swarms such as schooling fish or flocking birds.  ... 
doi:10.1007/978-3-642-04020-7_104 fatcat:x2d3k3o3mnaulfkspmvop4lnse

New Trends in Artificial Intelligence: Applications of Particle Swarm Optimization in Biomedical Problems [chapter]

Aman Chandra Kaushik, Shiv Bharadwaj, Ajay Kumar, Avinash Dhar, Dongqing Wei
2018 Intelligent System  
Hence, PSO algorithms is widely used in various research fields like ranging from artificial neural network training to other areas where GA can be used in the system.  ...  This method was designed by the researchers after inspired by social behavior of flocking bird or schooling fishes.  ...  Hence, aspects of algorithms for alignment of multiple sequences have been an awfully dynamic analysis field [12] .  ... 
doi:10.5772/intechopen.73606 fatcat:qzjb6tzw3belno6qvl3lht23h4

Swarm Intelligence Algorithms in Bioinformatics [chapter]

Swagatam Das, Ajith Abraham, Amit Konar
2008 Studies in Computational Intelligence  
An example of multiple sequence alignments that improved the algorithm presented by Feng and Doolittle [66] .  ...  A multiple sequence alignment (MSA) is a sequence alignment of three or more biological sequences, generally protein, DNA, or RNA.  ... 
doi:10.1007/978-3-540-76803-6_4 fatcat:aqxo2q2pzzbjpehpm4nh3fuxoa

Fragmented protein sequence alignment using two-layer particle swarm optimization (FTLPSO)

Nourelhuda Moustafa, Moustafa Elhosseini, Tarek Hosny Taha, Mofreh Salem
2017 Journal of King Saud University: Science  
This paper presents a Fragmented protein sequence alignment using two-layer PSO (FTLPSO) method to overcome the drawbacks of particle swarm optimization (PSO) and improve its performance in solving multiple  ...  sequence alignment (MSA) problem.  ...  Progressive alignment is used to align multiple sequences, by aligning each two sequences together, creating a guide tree based on the similarity score of each two pairs, and aligning all sequences one  ... 
doi:10.1016/j.jksus.2016.04.007 fatcat:qdlbqka3j5h5tbtcuas7qw2md4

A Hybrid Algorithm Using a Genetic Algorithm and Cuckoo Search Algorithm to Solve the Traveling Salesman Problem and its Application to Multiple Sequence Alignment

Ala'a Abu-Srhan, Essam Al Daoud
2013 International Journal of Advanced Science and Technology  
A 2-opt operation was added to the algorithm to improve the results. The suggested algorithm was applied to multiple sequence alignment and compared with the previous algorithms.  ...  In this paper, a cuckoo search optimizer (CS) is used along with a GA in order to avoid the local minima problem and to benefit from the advantages of both types of algorithms.  ...  multiple sequence alignment by using Clustalw and MSATSP.  ... 
doi:10.14257/ijast.2013.61.04 fatcat:s4cdj3cl3vdqpbcdfzeur47eaq

Efficient Two-Level Swarm Intelligence Approach for Multiple Sequence Alignment

Soniya Lalwani, Rajesh Kumar, Nilama Gupta
2016 Computing and informatics  
The issue addressed here is one of the most challenging multiple sequence alignment (MSA) problem.  ...  The two levels considered here are: to obtain optimal sequence length in level one and to attain optimum gap positions for maximal alignment score in level two.  ...  We gratefully acknowledge financial support by BTIS-sub DIC (supported by DBT, Government of India) to one of us (S.L.) and Advanced Bioinformatics Centre (supported by Govt. of Rajasthan) at Birla Institute  ... 
dblp:journals/cai/LalwaniKG16 fatcat:k4o46hbtbvcxfetfbseski5yy4

Classification of DNA Sequence Using Soft Computing Techniques: A Survey

K. Bhargavi, S. Jyothi
2016 Indian Journal of Science and Technology  
with multiple pattern alignment by using a genetic algorithmic program GA. 22 conferred a well-organized constrained multiple sequence alignment methodology through the secure performance. 23 Describe  ...  TS are a heuristic approach that aligns multiple sequences by using adaptive memory options.  ... 
doi:10.17485/ijst/2015/v8i1/89343 fatcat:3nxqk2efv5bkdmhilhmyup7noe

Bioinformatics: Strategies, Trends, and Perspectives [chapter]

Carlos Norberto, Adriane Beatriz de Souza Serapio
2010 New Advanced Technologies  
The automatic motif discovery problem is a multiple sequence local alignment problem that involves the search for approximate matches.  ...  Comparative genomic methods (Caspi & Pachter, 2006) seek for insertion regions where multiple alignments of genome sequences are disrupted by a large insertion in one or more species.  ... 
doi:10.5772/9441 fatcat:ph5rfy5d6fer5jblnoq7ihz5yq

Swarm Optimization Techniques for Segmenting Gel Electrophoresis Images

Sara Ibrahim Ibrahim, Mohamed Abd Allah Makhlouf, Ghada.S. El-Tawel, M. E. Wahed
2016 Current Research in Bioinformatics  
easy algorithm to implement.  ...  It also depends on swarm intelligence. PSO useful in image segmentation because the result is more exact and efficient.  ...  Step 2: Apply DNA Sequence alignment ClustalW for each sequence in the file. Step 3: Produced aligned file and apply a restriction enzyme to it that to cut DNA Sequence.  ... 
doi:10.3844/ajbsp.2016.18.33 fatcat:jxvcp2i4l5btjeznvcd5zdmjuq

Visual Tracking using Particle Swarm Optimization [article]

Rafid Siddiqui, Siamak Khatibi
2014 arXiv   pre-print
used in real applications.  ...  A novel approach toward solving planar template based tracking is proposed which performs a non-linear image alignment for successful retrieval of camera transformations.  ...  Particle Swarm Optimization (PSO) is an evolutionary algorithm which is directly inspired by the grouping behavior of social animals, notably in the shape of bird flocking, fish schooling and bee swarming  ... 
arXiv:1401.4648v1 fatcat:dzwn4v6mufgendhczrwsyd4nhm

ENHANCED BIO-INSPIRED ALGORITHM FOR CONSTRUCTING PHYLOGENETIC TREE

Jayapriya J., Selvaperumal P., Dhiliphan Rajkumar T.
2015 ICTACT Journal on Soft Computing  
This paper illustrates an enhanced algorithm based on one of the swarm intelligence techniques for constructing the Phylogenetic tree (PT), which is used to study the relationship between species.  ...  For results discussion, we used one of the standard dataset Treesilla. The results show that the Enhanced ABC (EABC) algorithm converges faster than others.  ...  The examples of the swarm are bees swarming around their hive; an ant colony is a swarm of ants; a flock of birds is a swarm of birds and crowds is a swarm of people [6] .  ... 
doi:10.21917/ijsc.2015.0147 fatcat:gx6occsgrvadzjeryu3hn5myq4

Path Planning Optimization for Agricultural Spraying Robots Using Hybrid Dragonfly – Cuckoo Search Algorithm

S. Muthukumaran, Manikandan Ganesan, J. Dhanasekar, Ganesh Babu Loganathan
2021 Alınteri Zirai Bilimleri Dergisi  
Here the agricultural routing problem is expressed as a Travelling Salesman Problem, and the simulations are performed to find the effectiveness of the proposed algorithm.  ...  The proposed algorithm has generated better results when compared with other computational techniques such as PSO in terms of both solution quality and computational efficiency.  ...  Levy flights are used to enhance stochastic behaviour in the exploration phase.  ... 
doi:10.47059/alinteri/v36i1/ajas21062 fatcat:3ji42sxfxfbxhdfc55mvehysci

Protein Secondary Structure Prediction using Deep Neural Network and Particle Swarm Optimization Algorithm

Angela U., Adetayo Sylvester
2018 International Journal of Computer Applications  
The basic particle swarm optimization algorithm was used in training a deep neural network as implemented using Java programming language with spring boot framework for generating the various APIs.  ...  Acids Sequence).  ...  Multiple Sequence Alignment (MSA) of the dataset was then generated with Psi-blast using UniRef90 dataset as the reference sequence.  ... 
doi:10.5120/ijca2018918070 fatcat:6x2iuygd2jenndnkw5wtv7oe7y

Clusterflock: a flocking algorithm for isolating congruent phylogenomic datasets

Apurva Narechania, Richard Baker, Rob DeSalle, Barun Mathema, Sergios-Orestis Kolokotronis, Barry Kreiswirth, Paul J. Planet
2016 GigaScience  
Because there is no central control, algorithms modeled on swarm intelligence excel at data mining tasks where the goal is discovery of unknown patterns in data.  ...  It is made available under a We have used the incongruence length difference (ILD) in our analysis of the Clusterflock algorithm, but the algorithm could also be applied to the likelihood ratio test 95  ...  Swarms are by definition leaderless and the agents are given no internal or external direction. Ant colonies, swarms of bees, shoals of fish, and flocks of birds all demonstrate this kind of ! 3!  ... 
doi:10.1186/s13742-016-0152-3 pmid:27776538 pmcid:PMC5078944 fatcat:bivl2sulorgn3cy26qd67njobu

Review of Different Sequence Motif Finding Algorithms

Fatma A Hashim, Mai S Mabrouk, Walid Al-Atabany
2019 Avicenna journal of medical biotechnology  
Over the past decades, different algorithms were used to design fast and accurate motif discovery tools.  ...  Nature-inspired algorithms and many of combinatorial algorithms are recently proposed to overcome these problems.  ...  Using population clustering technique, Paul et al 91 proposed an algorithm for PMP to detect multiple and weak motifs.  ... 
pmid:31057715 pmcid:PMC6490410 fatcat:jnytyp3ds5gwpdnuy6vwf7jevq
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