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Figure 7 | BMC Bioinformatics

Figure 7

From: MUSCLE: a multiple sequence alignment method with reduced time and space complexity

Figure 7

Additive profiles. The profile functions in MUSCLE require amino acid frequencies for each column. Here we show the alignment of two profiles X and Y, giving a new profile Z. Note that the count nZ i for amino acid i in a given column of Z is the sum of the counts in the child profiles, i.e. nZ i = nX i + nY i . In terms of frequencies, this becomes f Z i = NXf X i /NZ + NYf Y i /NZ, where NX, NY, NZ are the number of sequences in X, Y and Z respectively. Therefore, given a suitable sequence weighting scheme, it is possible to compute frequencies in Z from the frequencies in X and Y. This avoids the step of building an explicit multiple alignment for Z in order to compute frequencies, as done in CLUSTALW and MAFFT.

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