Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation.

E P Xing; D M Wolf; I Dubchak; S Spengler; M Zorn; I Muchnik; C Kulikowski

doi:10.1006/jtbi.2001.2319

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Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation.

E P Xing·D M Wolf·I Dubchak·S Spengler·M Zorn·I Muchnik·C Kulikowski

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Abstract

Automatic identification of sub-structures in multi-aligned sequences is of great importance for effective and objective structural/functional domain annotation, phylogenetic treeing and other molecular analyses. We present a segmentation algorithm that optimally partitions a given multi-alignment into a set of potentially biologically significant blocks, or segments. This algorithm applies dynamic programming and progressive optimization to the statistical profile of a multi-alignment in order to optimally demarcate relatively homogenous sub-regions. Using this algorithm, a large multi-alignment of eukaryotic 16S rRNA was analyzed. Three types of sequence patterns were identified automatically and efficiently: shared conserved domain; shared variable motif; and rare signature sequence. Results were consistent with the patterns identified through independent phylogenetic and structural approaches. This algorithm facilitates the automation of sequence-based molecular structural and evolutionary analyses through statistical modeling and high performance computation.

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Algorithms Animals Computational Biology Conserved Sequence Models, Genetic RNA, Ribosomal, 16S Sequence Alignment Journal Article

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E P Xing, D M Wolf, I Dubchak, S Spengler, M Zorn, I Muchnik, C Kulikowski. 2001-09-21. Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for multiple alignment segmentation.. https://doi.org/10.1006/jtbi.2001.2319

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