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PubMed · 8481822

Dot-plot comparisons by multivariate analysis (DOCMA): a tool for classifying protein sequences.

C Landès·A Hénaut·J L Risler
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Abstract

A method aimed at classifying protein sequences without resorting to pairwise alignment is presented. Called DOCMA (DOt-plot Comparisons by Multivariate Analysis), it is based on a multivariate analysis of the pairwise dot-plots between all the sequences in the set. The dot-plots are first simplified by considering only the projections of the 'diagonal' segments of similarity onto the axes. From these projections a data matrix is built, in which each column is representative of the comparisons of one given sequence with all the other ones. This data matrix is then transformed into a distance matrix by a chi-squared analysis, from which the coordinates of the sequences in an orthonormal Euclidean space are obtained. The sequences are finally classified by a dynamic clustering procedure followed by a search for strong clusters. Application of this method to protein families such as the globins, the cytochromes c and the aminoacyl-tRNA synthetases shows that it is quite effective in delineating subgroups that contain even distantly related sequences.

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AlgorithmsAmino Acid SequenceCluster AnalysisMultivariate AnalysisSoftwareJournal ArticleResearch Support, Non-U.S. Gov't

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BibTeXRIS

C Landès, A Hénaut, J L Risler. 1993. Dot-plot comparisons by multivariate analysis (DOCMA): a tool for classifying protein sequences.. https://doi.org/10.1093/bioinformatics%2F9.2.191

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