Iterative refinement of structure-based sequence alignments by Seed Extension |
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Authors: | Changhoon Kim Chin-Hsien Tai and Byungkook Lee |
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Institution: | (1) Laboratory of Molecular Biology, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892, USA |
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Abstract: | Background Accurate sequence alignment is required in many bioinformatics applications but, when sequence similarity is low, it is difficult
to obtain accurate alignments based on sequence similarity alone. The accuracy improves when the structures are available,
but current structure-based sequence alignment procedures still mis-align substantial numbers of residues. In order to correct
such errors, we previously explored the possibility of replacing the residue-based dynamic programming algorithm in structure
alignment procedures with the Seed Extension algorithm, which does not use a gap penalty. Here, we describe a new procedure
called RSE (Refinement with Seed Extension) that iteratively refines a structure-based sequence alignment. |
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Keywords: | |
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