Solving multiple sequence alignment problems by using a swarm intelligent optimization based approach

International Journal of Electrical and Computer Engineering (IJECE)
Vol. 13, No. 1, February 2023, pp. 1097~1104
ISSN: 2088-8708, DOI: 10.11591/ijece.v13i1.pp1097-1104  1097
Journal homepage: http://ijece.iaescore.com
Solving multiple sequence alignment problems by using a
swarm intelligent optimization based approach
Tirumala Paruchuri1,2
, Gangadhara Rao Kancharla2
, Suresh Dara3
1
Department of Management Information System, Jazan University, Kingdom of Saudi Arabia
2
Department of Computer Science and Engineering, Acharya Nagarjuna University, Andhra Pradesh, India
3
School of Technology, Woxsen University, Hyderabad, Telangana, India
Article Info ABSTRACT
Article history:
Received Apr 26, 2022
Revised Aug 9, 2022
Accepted Sep 5, 2022
In this article, the alignment of multiple sequences is examined through
swarm intelligence based an improved particle swarm optimization (PSO). A
random heuristic technique for solving discrete optimization problems and
realistic estimation was recently discovered in PSO. The PSO approach is a
nature-inspired technique based on intelligence and swarm movement. Thus,
each solution is encoded as “chromosomes” in the genetic algorithm (GA).
Based on the optimization of the objective function, the fitness function is
designed to maximize the suitable components of the sequence and reduce
the unsuitable components of the sequence. The availability of a public
benchmark data set such as the Bali base is seen as an assessment of the
proposed system performance, with the potential for PSO to reveal problems
in adapting to better performance. This proposed system is compared with
few existing approaches such as deoxyribonucleic acid (DNA) or ribonucleic
acid (RNA) alignment (DIALIGN), PILEUP8, hidden Markov model
training (HMMT), rubber band technique-genetic algorithm (RBT-GA) and
ML-PIMA. In many cases, the experimental results are well implemented in
the proposed system compared to other existing approaches.
Keywords:
Evolutionary computation
technique
Multiple sequence alignment
Optimization
Pairwise alignment
Particle swarm optimization
This is an open access article under the CC BY-SA license.
Corresponding Author:
Suresh Dara
School of Technology, Woxsen University
Hyderabad, Telangana, India
Email: darasuresh@live.in
1. INTRODUCTION
The methanesulfonic acid (MSA) is one of the most challenging and powerful tasks in solving
computational problems. Evaluating the biological sequences will helps in MSA process. MSA is defined by
the combination of amino acids and nucleotide sequences. Primary and secondary structures will be useful in
understanding the structure of a given sequence. MSA helps in finding the phylogenetic distance for a
particular sequence. In computational biology, the main task is to predict the order of the structure of a given
molecule [1], [2] and also MSA makes it more useful to find the structure. In computational biology, the
MSA will be useful for solving a variety of tasks. So, this is the main reason why researchers are more
focused on solving MSA problems effectively. The primary purpose of MSA is to differentiate sequences
with similar inactive properties. However, if possible, not only distinguish rows with inactive characters, but
also compare them with other characters. In bioinformatics, the main problem in MSA is knowing the
relationship between phylogenetic and genetics. So far, various methods have been used to overcome this
problem.
Recently, the nature inspired computing is very popular to solving kind of optimization problems,
particularly in MSA problems [3]. Especially, many algorithms are successfully applied to solving multiple

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sequence alignment problem. Lalwani et al. [4] introduced a new approach as two-level strategy for solving
MSA problem. A swarm intelligence-based optimization approach is used to solve MSA problem in [5].
To effectively solve MSA problems, a dynamic programming (DP) approach is useful. In DP, the
large domain scoring feature is used to update results for MSA issues. In 1970 the DP solution to the MSA
problem was proposed by Needleman and Wunsch [6]. Assuming that the number and length of sequences
increase, the DP approach will break easily. However, considering the time complexity and number of sof the
dynamic program approach also increases with increasing sequence length and number. So, the MSA
problem will led to NP-hard. Therefore, the major aim is to tackle MSA issues in an systematic manner i.e.,
similarities need to be developed among the sequences with less complexity. Another way to deal MSA
problems is to use a progressive alignment approach. However, it will be useful in solving because it is less
complex [6], [7]. According to this method, we first assume a similar sequence and then refer to a dynamic
set of those sequences. CLUSTAL W [8] is a classic approach in progressive methods.
Another approach is an iterative procedure used to solve MSA problems. It starts with an initial
alignment, filtering the frequent solutions until no possible improvement. Here, the decision does not depend
on the initial alignment. The target of the iteration process is to enhance the quality of alignment. Simulated
annealing is one type of iterative or stochastic method. A simulated annealing with particle swarm
optimization (PSO) is proposed for MSA problem [9], which mainly focus on global search by PSO and to
avoid the trapping in local optima is incorporated with simulated annealing.
Evolutionary algorithms (EAs) usually rely on population-based approach mainly focus on global
search. In MSA, EA will be useful in randomization, and the next EA step will be applied to the sequence to
improve similarity. Sequence alignment by genetic algorithm (SAGA) [10], rubber band technique-genetic
algorithm (RBT-GA) [11], and several other genetic algorithm (GA) algorithms are based on MSA. Using
reference sets 2 and 3, Taheri and Zomaya [11] solved 34 issues from the Bali database. In EA, local optimal
solutions achieve low variance, and this is considered a major disadvantage. DP is used in the proposed local
optimum solution method. We have an operator called inbuilt elitism in PSO. The proposed method of
elitism and initial operator modification will help to solve the MSA problem effectively.
Another swarm intelligent based approach is proposed by inspired from the artificial fish algorithm.
Dabba et al. [12] proposed multi objective artificial fish swarm algorithm called MOAFS for solving MSA
problem. Here, they proposed two fitness functions to maintain diversity in exploration and exploitation in
the search space. Chaabane et al. [13] proposed a hybrid approach for solving MSA as PSO with Tabu search
called PSO-TS. The PSO used effectively explore the search space and Tabu search used for produce the
global best solutions in high quality. A bird swarm align algorithm [14] also proposed for solving MSA
problem. Brainstorm optimization based algorithm with a dynamic population size is proposed for solving
MSA problem in [15], [16].
A hybrid approach is proposed in [17] which is combination of PSO and artificial bee colony (ABC)
optimization technique called hybrid algorithm of artificial bee colony and particle swarm optimization
(HABC-PSO). It integrates the Tent chaos search with opposition-based learning where they incorporate with
recombination operator technique, to gain best solutions by using this recombination operator. A multi
objective ABC proposed [18] for MSA problem, used two objective functions as one is sum of pairs and
another one is entropy. Another ABC based three level multi objective approach for ribonucleic acid (RNA)
multiple structural alignment problem [19]. A new kind approach based on flower pollination algorithm
(FPA) [20] is proposed for solving MSA problem, this metaheuristic approach used for finding the alignment
score based maximizing the sum of pairs and column score.
This article organizing as, required method PSO is discussed in section 2. The proposed method of
PSO was discussed in step by step briefly along with illustration of decoding and encoding in section 3. In
section 4, we discussed the proposed method experimental studies as well as comparison with other methods
in briefly. At last, we conclude the paper in section 5.
2. METHODS
Many evolutionary computation techniques have been successes fully used for solving optimization
problem. In this article we have adopted the one of the swarm intelligent based techniques is PSO. Finding
the right solution in a large search space is very useful. In 1995, Kennedy and Eberhart [21] was inspired by
schools of fish or birds. A binary version of PSO was introduced in [22] for MSA problem. We used same
kind of approach in out experimental study. The (1) and (2) describe velocity and position updates.
𝑉i,d(t + 1) = w ∗ 𝑉i,d(t) + c1 ∗ r1 ∗ (𝑝𝑏𝑒𝑠𝑡 − 𝑋i,d) + c1 ∗ r2 ∗ (𝑝𝑏𝑒𝑠𝑡gbest,d − 𝑋i,d) (1)

Int J Elec & Comp Eng ISSN: 2088-8708 
Solving multiple sequence alignment problems by using a swarm intelligent … (Tirumala Paruchuri)
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𝑋i,d(t + 1) = 𝑋i,d(t) + 𝑉i,d(t + 1) (2)
Where X is the current position, r1 and r2 are represented as random vectors in [0,1], V is shown as particle
velocity, c1 and c2 represented as accelerating constants, t is considered as iteration, and w represents the
inertial weight.
3. PROPOSED APPROACH
This section going to discuss the proposed method of PSO and explained the process in step by step.
The following steps are explained as: initializing the position of the particle, how representation as particle
and how updating the particle position through velocity and (1), (2). Given a complete description of
proposed fitness function, and calculation of alignment score. The explanation of this particular steps is
discussed below.
3.1. Initial generation
The development of some initial solutions is considered the main goal. However, initial solutions
can be developed by providing gaps between the residues. The following example shows the generation of
the initial population. Figure 1(a) shows the initial MSA. From each pair we find pairwise alignment using
the Wunsch and Needleman algorithms. In Figure 1(b) shows the initial pair (1, 2). Then, pairwise alignment
for the initial pair (1, 2) need to be find, which was shown in Figure 1(c). Suppose if the problem is with 4
sequences, then 4*(4-2)/2=6 pairs are considered. So pairwise alignment must be found in the same way for
each pair. Now random permutation from 1 to N must be generated. For example, if we have 4 sequences,
any permutation from 1 to 4 can be generated. If every permutation of (3, 4, 1 and 2) is generated then
Figure 1(d) shows the alignment process. K solutions can be generated by K times of random permutations
from 1→N. At this stage, the initial population is developed.
(a) (b) (c) (d)
Figure 1. An illustration of generate an initial solution (a) initial MSA, (b) initial pair (1, 2), (c) pairwise
alignment for the initial pair (1, 2), and (d) alignment process
3.2. Solution representation as a particle
Each and every solution was represented in PSO as particle.
𝑋i, = 𝑋1, 𝑋2, … . . 𝑋d where 1≤I≥N.
Where d is the dimension size in a particle, N represents the number of particles. Out of the 200 solutions we
record one solution and explain how we can encode the MSA problem into a particle. Figure 2 shows the
initial solution.
Binary encoding schematic-in this part of the schematic, place 1 at the gap position and 0 at the
protein sequence position. This is shown in Figure 2 showing how the initial solution is encoding a particle.
In each column we see decimal values from bottom to top with binary encoded values. So, X1=(1, 0, 0, 8, 4,
and 2) is a solution for this particle representation. Therefore, in MSA, the number of columns is equal to the
number of dimensions in the particle. In MSA, with the encoding scheme, new particles are only developed
after the initial solution generation.
3.3. Fitness function
MSA utilize the weighted sum of pair method (WSPM) function to calculate the fitness
measurement. In this, score for every column is equal to the computation of product of every pair symbol
score.

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𝑆 = ∑𝐿
𝑖=1 𝑆l, (3)
𝑆l, = ∑𝑁−1
𝑖=1 ∑𝑁
𝑗=1+1 (𝑊ij 𝐶𝑜𝑠𝑡 (𝐴i,𝐴j,)) (4)
The overall alignment score is computed against the column scores through (3). Where l indicates the number
of columns in the total alignment, S indicates the MSA cost. N represents the sequence count, Sl represents
the value for the lth
column of length l, Wij represents the weights of the rows for i and j. Its main purpose is
to explain the variance between the two sequences.
Wij=(Miss)/(TL)
Where, Miss count of mismatch characters in the alignment, TL lengh of total align. Cost(Ai, Aj) is a function
use to calculate the alignment score og two aligned sequences Ai and Aj. Here, there are four possible cases.
(1) When Ai ≠ “_” and Aj ≠ “_” then cost (Ai, Aj) was explained from the acceptable mutation’s matrix
percentage. The (2) suppose Ai= “_” and Aj= “_” then cost (Ai, Aj)=0. The (3) and (4) at last, cost (Ai, Aj) is
the cost function, which considers the summing of substitution costs like deletions or insertions takes place if
Ai= “_” and Aj≠ “_” or viseversa then cost (Ai, Aj)=1.
Figure 2. The binary encoding process from initial solution
3.4. An alignment calculation
If 5 solutions were taken in the initialization process and in each dimension, every particle is
assigned with initial velocity i.e., 0. Later in the initialization process, out of a total of 100 solutions,
1 solution has been shown in Figure 3. Based on encoding scheme, such solution turned into a particle
(2, 8, 0, 0, 5). For every particle, we find the particle in the similar manner.
Figure 3. Initial alignment
Suppose the remaining particles solutions are P1=(2, 8, 0, 0, 5), P2=(0, 4, 4, 0, 0), P3=(3, 5 1, 2, 4)
P4=(4, 2, 1, 8, 1), and P5=(9, 1, 5, 3, 4). The calculate the pbest values as pbest1=(8, 4, 2, 1,1),
pbest2=(6, 2, 4, 3, 8), pbest3=(5, 3, 7, 0, 2), pbest4=(2, 2,8, 0, 4), and pbest5=(6, 1, 8, 2, 2). Later, find the
fitness value of each particle by using (3) suppose after calculating the fitness value for five particles the
values like Fit (P1)=13, similarly 19, 18, 7, 15,13, and 19 for respective particle fitness values. Then, the
Fit (pbest1)=13, Fit (pbest2)=19, Fit (pbest3)=18, Fit (pbest4)=7, and Fit (pbest5)=15.

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Update the particle position and velocity: Through (1) and (2), we need to update the position and
velocity.
𝑉i,d(t + 1) = 0.691 ∗ 0 + 2.15 ∗ 0.35 ∗ (2 − 2) + 2.22 ∗ 0.46 ∗ (4 − 2)
=0+0 +2.042
=2.042
Now calculate of the new position
𝑋i,d(t + 1) = 𝑋i,d(t) + 𝑉i,d(t + 1)
=2+2.042= 4.042
=4
Here, updated position of floor value is considered due to the presence of discrete valued function in
encoding scheme. However, 4 is the updated position, then every particle in each dimension gets updated in
the similar manner. Hence, we will get new particles like P1=(4, 0, 3, 0, 2), P2=(4, 2, 4, 1, 2), P3=(2, 4, 0, 1,
2), P4=(3, 6, 0, 1, 4), and P5=(1, 5, 0, 1, 4). Also, fitness value for new particles can be foundFit (P1)=44,
Fit (P2)=5, Fit (P3)=12, Fit (P4)=30, and Fit (P5)=10. Later, pbest value can be updated through the
algorithm which is provided in Algorithm 1. The gap can be provided based on decoding scheme, which is
explained in Figure 4(a). Later, protein sequences can be allotted in specific positions to produce the final
MSA. Figure 4 (b) determines the final MSA.
Algorithm 1. The PSO approach for MSA problem
1 Initialize the random solutions as particles with X and V values for N solutions
2 Calculate fitness value for each particle using (3), find pbest
3 Begin
4 for i=1 to N;
5 If (Fit (Pi)>Fit (pbesti)//update pbest
6 pbesti=Pi;
7 End If
8 End for
9 repeats from 3 until finite number of iterations
10 End
(a) (b)
Figure 4. A sample solution in a iteration (a) a decoding scheme and (b) final updated MSA
4. RESULTS AND DISCUSSION
In this section, we have implemented the propose approach and the results are examined and then
compared with the few existing methods. The parameter setting of PSO are considered as N=200,
Vmax=2Number of sequences
, Vmin=0, w=0.758, c1=2.15, c2=2.22, r1 and r2 are a random value in [0,1]. Here, the
performance of our proposed approach is compared with few existing approaches using different reference
datasets. The compared results presented in Tables 1 and 2.
4.1. Comparative performance of proposed method
In our experiments, we tool a benchmark dataset from publicly available database Benchmark
alignment dataBASE (BaliBASE) [23], [24]. Randomly 16 datasets have picked from the database. So, 12
datasets are from reference set 2 and remaining 4 datasets are from reference set 3. The existing results are
taken from the literature RBT-GA [11]. Also the experimental results compared with literature [25].

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4.2. Experimental results in BAliBASE reference 2 datasets
From such reference, 12 datasets were extracted. All of these sets are different with respect to the
terms of number and length. Our proposed method is well compared with various existing approaches like
ML-PIMA, DIALIGN, rubber band technique-genetic algorithm (RBT-GA), hidden Markov model training
(HMMT) and PILEUP-8 for evaluating the proposed method performance. Table 1, presented the results
reference 2 datasets, and it determines that the proposed method performed well in 12 datasets and existing
methods in 7 test cases. Also, the proposed approach does not achieve best solution within 5 test cases but it
just closely related towards the best solution. Finally, Table 2 explains that the entire performance of the
proposed system performed well than the other existing methods in reference 3 datasets. The proposed
approach score was 0.708 whereas other approaches are an average less than 0.3. only one approach getting
good results than our proposed approach that is RBT-GA which reported as 0.83.
Table 1. Result comparison in reference 2 dataset
Datasets DIALI PILEUP-8 HMMT RBT-GA ML-PIMA Proposed Approach
2trx 0.734 0.87 0.739 0.982 0.702 0.787
1r69 0.675 0.45 0 0.9 0.675 0.251
1sbp 0.043 0.177 0.214 0.778 0.054 0.817
1csy 0 0.114 0 0.735 0 0.797
1wit 0.724 0.476 0.641 0.825 0.463 0.757
1tvxA 0 0.345 0.276 0.891 0.241 0.534
1aboA 0.384 0 0.724 0.812 0.22 0.838
1idy 0 0 0.353 0.997 0 0.559
1havA 0 0.493 0.194 0.792 0.238 0.817
1uky 0.216 0.562 0.395 0.625 0.306 0.719
1tgxA 0.63 0.318 0.622 0.835 0.543 0.886
1ubi 0 0 0.053 0.795 0.129 0.799
Avg score 0.283 0.317 0.35 0.83 0.297 0.708
4.3. Experimental results in BAliBASE reference 3 datasets
Within reference set 3, we have considered 4 datasets lidy, luky, lr69 and lubi out of 12 datasets.
Table 2 describes the experimental results on reference 3 test cases that performed better and 1 test case did
not perform well but it almost closes to the best. However, Table 2 shown the proposed approach was
outperformed with better average solutions than existing methods. Table 2 shows that the comparative results
on [3] dataset with few existing algorithms. The results are considered as average score, the proposed
approach claim as 0.514, at same time other approaches reported RBT-GA as 0.395, and the next highest was
ML-PIMA as 0.263, all other approaches were reported very less score comparing with our proposed
approach.
Table 2. Result comparison on reference 3 dataset
Datasets DIALI PILEUP-8 HMMT RBT-GA ML-PIMA Proposed approach
1idy 0 0 0.227 0.548 0 0.623
1uky 0.139 0.083 0.037 0.35 0.148 0.411
1r69 0.524 0 0 0.374 0.905 0.425
1ubi 0 0.268 0.366 0.31 0 0.598
Avg score 0.165 0.087 0.157 0.395 0.263 0.514
5. CONCLUSION
This article is mainly discussed about an improved PSO for solving the alignment problem. Also,
experiments have conducted in multiple times to evaluate the performance of proposed system. Meanwhile in
PSO approach, an initial operator is used for evaluating. Also, initial operator is improved with more efficacy
and dominance. The weighted pair function was used in the proposed system for fitness calculation. The
powerful datasets have taken from public database i.e., BaliBASE with 2.0 version, which was explained the
efficacy of the RBT-GA algorithm. Later, better solutions of Bali score have taken for comparison with
various existing methods. In most of the test results, the proposed system performed best and, in few cases,
the performance is slightly lacked but it almost closes to the solution. The major reason in utilizing the
improved initial operator was to improve the proposed system efficacy. Therefore, we claim that our
proposed system shown better results than the existing approaches.

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BIOGRAPHIES OF AUTHORS
Tirumala Paruchuri she obtained her Masters in Computer Applications (Sri
Krishna Devaraya University, Anantapur, India) and Masters in Technology-Computer
Science and Engineering (Jawaharlal Nehru Technological University, Hyderabad, India). She
started her career in teaching with St. Mary’s College of Engineering and Technology,
Hyderabad, India and presently teaching in the department of Management Information
System, Jazan University, Jazan, Kingdom of Saudi Arabia and also pursuing her research
(Ph.D.) in Acharya Nagarjuna university, Guntur, India. Her research interests are data mining,
machine learning, cloud computing, evolutionary computing, and big data analytics. She can
be contacted at email: tirumalaparuchuri@gmail.com.

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Gangadhara Rao Kancharla Professor Gangadhara Rao did his B.Tech in
Electrical and Electronics Engineering later he did his M.Tech in Computer Science. He was
awarded his Ph.D. in Computer Science for the thesis titled “Analytical and Game theoretical
approach of TCP SYN flooding for web server”. Several research scholars working under him
in the areas of AI&ML. Cloud computing, big data and Manets. He has published many
research articles in reputed journals. He has advisory member of many reputed international
conferences. He can be contacted at email: kancherla123@gmail.com.
Suresh Dara he is currently working as a Professor in B V Raju Institute of
Technology, Narsapur, Medak-502313, India. He has completed his Ph.D. from Indian
Institute of Technology (ISM), Dhanbad, India in 2015, completed his Masters in CST from
Andhra University, India in 2008. He has published many research articles in reputed journals,
international conferences, Books and Book chapters. He served as reviewer for many reputed
journals. His current research interests are soft computing, machine learning, deep learning,
evolutionary computation, and bioinformatics. He has committee member of many reputed
international conferences and workshops. He can be contacted at email: darasuresh@live.in.

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