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Anomalous matrices can correct overextension because alignment boundary correction is robust to matrix selection.
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Using a shallower scoring matrix that targets the correct sequence identity can correct overextension (Fig. 4).
Adjusting the scoring matrix to reflect the identity of the homologous sequence can correct higher identity overextended alignment boundaries.
Therefore, one can correct for covariates by simply pre- and postmultiplying N(2) × N matrices, by appropriate projection matrices.
Predicting the scoring matrix that will lead to a better alignment, using initial (possibly overextended) identity given by BLOSUM62, can correct overextended alignments.
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