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Those HBs which did not contain at least one significantly conserved position (conservation level > 0) were discarded.
It is difficult to dig out detailed information from the position conservation correlation matrix R(con)L×L of PDZ database, because too many conservative positions complicate the analysis.
The alignment is represented in five default colour schemes based on: residue type, position conservation, position reliability, residue hydrophobicity and secondary structure; depending on the options set.
The position conservation correlation matrix can be derived from the reduced position frequency matrix FM×L.
Then the position conservation correlation matrix and position mutation correlation matrix is constructed from the amino acid position mutative equation.
Fig. 2 B is the contour map of position conservation correlation matrix R(con)L×L of PDZ database.
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A computational approach, namely amino acid position conservation-mutation correlation analysis (CMCA), is developed to predict mutually mutative positions and find the evolutionary network in protein family.
In this study a computational approach, namely amino acid position conservation-mutation correlation analysis (CMCA), is developed to predict mutually mutative positions and find the evolutionary network in protein family.
The position mutations are equally important to the position conservations for study of functional evolution of protein family.
Unlike traditional SCA (statistical coupling analysis) approach, which is based on the statistical analysis of position conservations, the CMCA focuses on the correlation analysis of position mutations.
Unlike traditional SCA (statistical coupling analysis) approach [2], [15], [16], [17], which is based on the statistical analysis of position conservations, the CMCA focuses on the correlations of position mutations in a protein evolutionary family.
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