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Creating a Repeat entry
Creating a Repeat type entry in Pfam broadly follows the same process as creating other entry types, with the exception of threshold adjustment and boundaries determination. These two steps pose a more arduous task in cases of repeat units compared to domains. This is due to the sequence divergence and short length of repeat sequences.
Detecting repeats by profile HMMs involves careful, manual curation and fine tuning of different parameters (allowance of inserts, deletes and amino acid mismatches in the seed alignments, E-values and bit-scores for profile HMMs) in order to account for the intricacies of repeats. The process is explained in more detail in the following pages (Threshold adjustment and Boundaries determination).