Prediction of Protein Function Using Ant Colony Sequence Alignment

2011 ◽  
Vol 8 (10) ◽  
pp. 2155-2158
Author(s):  
Qingguang Zeng ◽  
Bo Liao ◽  
Hao Liu ◽  
Dachao Li ◽  
Renfa Li
Keyword(s):  
Sequence Alignment ◽  
Protein Function ◽  
Ant Colony

scholarly journals Orderly Roulette Selection Based Ant Colony Algorithm for Hierarchical Multilabel Protein Function Prediction

2017 ◽  
Vol 2017 ◽  
pp. 1-15 ◽  
Author(s):  
Zhengping Liang ◽  
Rui Guo ◽  
Jiangtao Sun ◽  
Zhong Ming ◽  
Zexuan Zhu
Keyword(s):  
Ant Colony Optimization ◽  
Protein Function ◽  
Ant Colony Algorithm ◽  
Protein Function Prediction ◽  
Function Prediction ◽  
Ant Colony ◽  
Classification Model ◽  
Selection Strategy ◽  
Classification Rules ◽  
Ant Colony Optimization Algorithm

Ant colony optimization (ACO) algorithms have been successfully applied to identify classification rules in data mining. This paper proposes a new ant colony optimization algorithm, named hmAntMinerorder, for the hierarchical multilabel classification problem in protein function prediction. The proposed algorithm is characterized by an orderly roulette selection strategy that distinguishes the merits of the data attributes through attributes importance ranking in classification model construction. A new pheromone update strategy is introduced to prevent the algorithm from getting trapped in local optima and thus leading to more efficient identification of classification rules. The comparison studies to other closely related algorithms on 16 publicly available datasets reveal the efficiency of the proposed algorithm.

scholarly journals An Application of the Eigenproblem for Biochemical Similarity

Symmetry ◽  
2021 ◽  
Vol 13 (10) ◽  
pp. 1849
Author(s):  
Dan-Marian Joiţa ◽  
Mihaela Aurelia Tomescu ◽  
Donatella Bàlint ◽  
Lorentz Jäntschi
Keyword(s):  
Amino Acids ◽  
Sequence Alignment ◽  
Protein Function ◽  
Scoring Function ◽  
Essential Amino Acids ◽  
Alignment Algorithm ◽  
Protein Alignment ◽  
Correct Alignment ◽  
Distance Matrices ◽  
Cartesian Coordinate

Protein alignment finds its application in refining results of sequence alignment and understanding protein function. A previous study aligned single molecules, making use of the minimization of sums of the squares of eigenvalues, obtained for the antisymmetric Cartesian coordinate distance matrices Dx and Dy. This is used in our program to search for similarities between amino acids by comparing the sums of the squares of eigenvalues associated with the Dx, Dy, and Dz distance matrices. These matrices are obtained by removing atoms that could lead to low similarity. Candidates are aligned, and trilateration is used to attach all previously striped atoms. A TM-score is the scoring function that chooses the best alignment from supplied candidates. Twenty essential amino acids that take many forms in nature are selected for comparison. The correct alignment is taken into account most of the time by the alignment algorithm. It was numerically detected by the TM-score 70% of the time, on average, and 15% more cases with close scores can be easily distinguished by human observation.

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