Profile-profile alignment. Two profiles (multiple sequence alignments) X and Y are aligned to each other such that columns from X and Y are preserved in the result. Columns of indels (gray background) are inserted as needed in order to align the columns to each other. The score for aligning a pair of columns is determined by the profile function, which should assign a high score to pairs of columns containing similar amino acids.
Edgar BMC Bioinformatics 2004 5:113 doi:10.1186/1471-2105-5-113