Multiple sequence alignment (MSA) is essential in phylogenetic, evolutionary and functional analysis. Several MSA tools are available in the literature. Here, we use several MSA tools such as
ClustalX, Align-m, T-Coffee, SAGA, ProbCons, MAFFT, MUSCLE and DIALIGN to illustrate comparative phylogenetic trees analysis for two datasets. Results show that there is no single MSA tool that
consistently outperforms the rest in producing reliable phylogenetic trees.
This paper proposes a clustering algorithm based on the Self Organizing Map (SOM) method. To find the optimal number of clusters, our algorithm uses the Davies Bouldin index which has not been used previously in the multi-SOM. The proposed algorithm is compared to three clustering methods based on five databases. Results show that our algorithm is as performing as concurrent methods.
The fundamental aim of protein classification is to recognize the family of a given protein and determine its biological function. In the literature, the most common approaches are based on sequence or structure similarity comparisons. Other methods use evolutionary distances between proteins. In order to increase classification performance, this work proposes a novel method, namely Consensus, which combines the decisions of several sequence and structure comparison tools to classify a given structure. Additionally, Consensus uses the evolutionary information of the compared structures. Our method is tested on three databases and evaluated based on different criteria. Performance evaluation of our method shows that it outperforms the different classifiers used separately and gives higher classification performance than a free-alignment method, namely ProtClass.
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