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Updated: Aug 19, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 6, 2014
Automatic discovery of sub-molecular sequence domains in multi-aligned sequences: a dynamic programming algorithm for
E P Xing1, D M Wolf, I Dubchak
1Center for Bioinformatics and Computational Genomics, NERSC, Berkeley, CA 94720, USA.
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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