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. Author manuscript; available in PMC: 2014 Oct 15.
Published in final edited form as: Curr Protoc Bioinformatics. 2013 Oct 15;43:3.5.1–3.5.9. doi: 10.1002/0471250953.bi0305s43

Figure 2. Comparison of a “shallow” (VTML 20) and “deep” (BLOSUM62) scoring matrix.

Figure 2

Both matrices are scaled in 1/2-bits. For the small part of the matrices shown here, the VTML20 matrix produces an average 2.80 half-bit identity score, and an average −0.59 non-identical score (weighted by amino-acid abundance). In contrast, BLOSUM62 produces 1.86 for identities but only −0.06 for non-identities. Thus, VTML20 targets shorter, higher-identity alignments, because it penalizes non-identities much more strongly.