Optimizing substitution matrix choice and gap parameters for sequence alignment |
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Authors: | Robert C Edgar |
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Institution: | (1) 45 Monterey Dr, Tiburon, CA 94920, USA |
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Abstract: | Background While substitution matrices can readily be computed from reference alignments, it is challenging to compute optimal or approximately
optimal gap penalties. It is also not well understood which substitution matrices are the most effective when alignment accuracy
is the goal rather than homolog recognition. Here a new parameter optimization procedure, POP, is described and applied to
the problems of optimizing gap penalties and selecting substitution matrices for pair-wise global protein alignments. |
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Keywords: | |
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