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Figure 5 | BMC Bioinformatics

Figure 5

From: H2r: Identification of evolutionary important residues by means of an entropy based analysis of multiple sequence alignments

Figure 5

Modes of handling gaps. For a correlation analysis, gaps cannot be treated like an additional amino acid. Otherwise e.g. column-pairs (1, 2), (1, 3), and (2, 3) would be predicted as possessing a strong coupling signal. Columns 4 – 6 illustrate the computation of frequencies f ( a i k , a j l ) MathType@MTEF@5@5@+=feaafiart1ev1aqatCvAUfKttLearuWrP9MDH5MBPbIqV92AaeXatLxBI9gBaebbnrfifHhDYfgasaacPC6xNi=xH8viVGI8Gi=hEeeu0xXdbba9frFj0xb9qqpG0dXdb9aspeI8k8fiI+fsY=rqGqVepae9pg0db9vqaiVgFr0xfr=xfr=xc9adbaqaaeGaciGaaiaabeqaaeqabiWaaaGcbaGaemOzayMaeiikaGIaemyyae2aa0baaSqaaiabdMgaPbqaaiabdUgaRbaakiabcYcaSiabdggaHnaaDaaaleaacqWGQbGAaeaacqWGSbaBaaGccqGGPaqkaaa@3839@ for H2r. All sequences containing a gap at position i or j were removed. In the case of columns i = 4, j = 5 it is one sequence (labelled red). For the determination of frequencies in columns i = 5 and j = 6, four sequences have to be removed (labelled green).

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