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Proteins are macromolecules essential for the structuring and functioning of living cells. Proteins generally have different functional regions which are conserved along evolution and are commonly termed as “functional motifs” or “domains”. Domains/motifs are found in different proteins and combinations and, as such, are functional protein subunits above the raw amino-acid level. Domain identification is thus an essential task in bioinformatics. Different strategies can be used to identify these regions of a target protein. Profile analysis, also known as sequence-profile comparison, is a powerful method. To identify new protein domains, an important database is used to compute a score that measures the similarity between the sequence and the domain. If the score is above a predefined threshold, the presence of the domain in the protein can be asserted. However this method may miss several domains when applied to an organism that is phylogenetically distant from the species used.
(Menichelli et al., 2018) Improving pairwise comparison of protein sequences with domain co-occurrence. PLoS Comput Biol.