Clustering of protein families into functional subtypes using Relative Complexity Measure with reduced amino acid alphabets |
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Authors: | Aydin Albayrak Hasan H Otu Ugur O Sezerman |
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Institution: | (1) Biological Sciences and Bioengineering, Sabanci University, Orhanli, Tuzla, Istanbul, Turkey;(2) Department of Medicine, BIDMC Genomics Center, Harvard Medical School, Boston, MA 02115, USA;(3) Department of Bioengineering, Istanbul Bilgi University, 34060 Istanbul, Turkey |
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Abstract: | Background Phylogenetic analysis can be used to divide a protein family into subfamilies in the absence of experimental information.
Most phylogenetic analysis methods utilize multiple alignment of sequences and are based on an evolutionary model. However,
multiple alignment is not an automated procedure and requires human intervention to maintain alignment integrity and to produce
phylogenies consistent with the functional splits in underlying sequences. To address this problem, we propose to use the
alignment-free Relative Complexity Measure (RCM) combined with reduced amino acid alphabets to cluster protein families into
functional subtypes purely on sequence criteria. Comparison with an alignment-based approach was also carried out to test
the quality of the clustering. |
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Keywords: | |
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