HHrepID is a novel automated procedure for the de novo identification of repeats in protein sequences. It is able to detect the sequence signature of structural repeats in many proteins that have not yet been known to possess internal sequence symmetry, such as TIM barrels and outer membrane beta-barrels. HHrepID uses HMM-HMM comparison to exploit evolutionary information in the form of the multiple sequence alignment of homologs, but in contrast to HHrep, the new method has several novel characteristics: (1) automated generation of a multiple alignment of repeats; (2) utilization of the transitive nature of homology through a novel merging procedure based on the fully probabilistic treatment of alignments; (3) superior alignment quality through an algorithm that maximizes the expected accuracy of an alignment; (4) the ability to identify different repeats within complicated architectures or multiple domains through automatic domain boundary detection, (5) new statistical treatment yielding improved sensitivity.
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Biegert A, Söding J:
HHrepID: de novo protein repeat identification by probabilistic consistency
Bioinformatics 2008 24(6), 807-814.