WOOF (Word-oriented objective function) is a method designed to rigourously apply the principle of visual alignment validation. WOOF does not actually make changes to a multiple sequence alignment, but is intead intended to choose the best alignment of a set of proteins from a set of such alignments that have been generated using different algorithms and parameter settings. The winning alignment is the one that best aligns a set of conserved patterns extracted using a pattern-finding approach such as TEIRESIAS. Patterns are weighted based on their statistical significance and position relative to other patterns.
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Beiko, R.G., Chan, C.X., and Ragan, M.A. (2005)
A word-oriented approach to alignment validation
Bioinformatics 21: 2230-2239