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Motivation: Profile-based protein homology detection algorithms are valuable tools in genome annotation and protein classification. By utilizing information present in the sequences of homologous proteins, profile-based methods are often able to detect extremely weak relationships between protein sequences, as evidenced by the largescale benchmarking experiments such as CASP and LiveBench. Results: We study the relationship between the sensitivity of a profile-profile method and the size of thedoi:10.1093/bioinformatics/btn097 pmid:18337259 fatcat:h2efqo2mcvbrbaebixf4wt5sdi