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27 lines
1.3 KiB
Text
27 lines
1.3 KiB
Text
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CAFS: Clustering Analysis of Functional Shifts
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CAFS is a simple and fast method for Clustering functionally divergent (FD)
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genes by Functional Category.
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The method implemented in CAFS is one of several sequence-based methods
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for identifying the 'interesting' subset of substitutions that might
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underpin functional divergence. These methods are based on the idea of that
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functionally-important residues are highly conserved, so that evolutionary
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rates tend to be low at important sites. Functional divergence can then be
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identified by comparing rates (or levels of conservation) between two
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clades of proteins at a homologous site. Alternatively, a significant
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change in amino acid identity (such as a large, positively-charged residue
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in one group of sequences versus a small, neutral residue in the other)
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could indicate functional divergence even without a change in rate.
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This program analyses alignments and provides the user with the best
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putative sites under functional divergence.
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NOTE: This only repackages the 64bit binary provided from upstream. A 32bit
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executable is not available.
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Citing:
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Caffrey BE, Williams TA, Jiang X, Toft C, Hokamp K, Fares MA (2011).
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Proteome-wide analysis of functional divergence in bacteria: Exploring a
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host of ecological adaptations.
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