Journal of Jilin University(Engineering and Technology Edition) ›› 2022, Vol. 52 ›› Issue (12): 2984-2993.doi: 10.13229/j.cnki.jdxbgxb20210538

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Multiple sequence alignment of proteins based on slime mold algorithm

Xin-lu WANG1,2,3(),Da-you LIU1,2(),Si-han LIU1,3,Zheng WANG1,2,Li-wei ZHANG1,2,Sa DONG1,2   

  1. 1.College of Computer Science and Technology，Jilin University，Changchun 130012，China
    2.Key Laboratory of Symbolic Computation and Knowledge Engineering，Ministry of Education，Jilin University，Changchun 130012，China
    3.College of International Education，Jilin University，Changchun 130012，China
  • Received:2021-06-18 Online:2022-12-01 Published:2022-12-08
  • Contact: Da-you LIU E-mail:xinlu@jlu.edu.cn;liudy@jlu.edu.cn

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Abstract:

Based on the slime mold algorithm （SMA）， an effective matching model （SMA_MSA） was developed to assist bioscientists in judging whether different sequences have homology， so as to predict protein structure. SMA_MSA and some other well-known competing algorithms were tested in the six data sets of BAliBASE 3.0. The results clearly show that SMA_SMA has excellent matching ability in the 31 data sets， indicating that the proposed model has great development potential in the problem of protein multiple sequence alignment.

Key words: computer application, protein sequence alignment, slime mold algorithm, BAliBASE

CLC Number: 

  • TP391

Fig.1

Description of MSA insertion vacancy"

Table 1

Effect of penalty score setting on sequence matching"

开放空位罚分扩展空位罚分作用
大大极少插入或插入，用于亲缘接近的蛋白质序列比对
大小少量较长空位插入，用于可能在整个功能域插入空位的情况
小小大量短的空位插入，用于亲缘关系疏远的蛋白质序列比对

Fig.2

BLOSUM62 scoring matrix"

Fig.3

Illustration of open space and extended space"

Fig.4

Example of protein multiple sequence alignment"

Table 2

SP values of each algorithm for solving multiple sequence comparisons"

数据集SNminLmaxLSP
DE算法GWO算法PSO算法SMA算法
BB11

BB11001

BB11008

BB11010

BB11012

BB11013

BB11015

BB11017

BB11021

BB11025

BB11035

4

4

4

4

5

4

4

4

4

5

83

104

490

320

51

297

247

102

64

71

91

540

492

397

101

327

264

139

103

138

1

0.25

0.91

1

1

0.92

1

0.56

1

1

1

0.75

0.91

1

1

0.92

1

0.56

1

1

1

0.25

0.91

1

1

0.75

0.86

0.44

1

0.67

1

1

0.91

1

1

0.92

0.93

0.56

1

1

Mean----0.860.910.790.93
BB12

BB12002

BB12003

BB12005

BB12006

BB12009

BB12012

BB12018

BB12020

BB12021

BB12022

6

8

9

4

5

4

4

4

6

5

165

58

197

220

67

298

752

118

71

79

231

85

234

242

201

548

974

129

85

475

1

0.88

1

1

1

0.97

0.98

0.94

1

0.89

0.88

0.75

0.9

1

1

0.97

0.98

0.94

1

1

1

0.63

0.9

1

1

0.89

0.97

0.76

1

0.72

0.88

0.88

0.8

1

1

1

0.98

0.94

1

0.89

Mean----0.970.940.890.94
BB20

BB20006

BB20030

51

47

224

76

293

155

0.33

1

0.22

1

0.44

1

0.56

1

Mean----0.670.610.720.78
BB30

BB30010

BB30018

BB30024

50

78

69

503

372

226

1293

688

982

0.69

0.78

0.61

0.82

0.72

0.59

0.85

0.72

0.60

0.88

0.81

0.76

Mean----0.690.710.720.82
BB40

BB40010

BB40025

BB40028

9

14

22

67

247

247

214

527

759

1

0.92

0.52

1

0.92

0.33

1

0.92

0

1

0.92

0.67

Mean----0.810.750.640.86
BB50

BB50004

BB50010

BB50013

9

17

18

386

372

230

505

688

318

0.71

0.25

0.73

0.76

0.25

0.6

0.68

0.25

0.6

0.71

0

0.27

Mean----0.560.540.510.33

Fig.5

Convergence curves of SP values obtained by the four algorithms on different data sets"

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