Rapid automatic detection and alignment of repeats in protein sequences

By Andreas Heger, Liisa Holm. Proteins: Structure, Function, and Bioinformatics, 2000

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Protein repeats: structures, functions, and evolution. (2001, methodology): “Useful implementations of this have recently been described (Pellegrini et al., 1999; Heger and Holm, 2000).”
De novo identification of highly diverged protein repeats by probabilistic consistency (2008, methodology): “Six methods belong to this class: internal repeat finder (Sonnhammer et al., 1998), PROSPERO (Mott, 2000), REPRO (Heringa and Argos, 1993), RADAR (Heger and Holm, 2000), TRUST [the successor of REPRO, Szklarczyk and Heringa (2004)], and the HHrep server (Söding et al., 2006).”
Structure and Function of the Bacterial Root Microbiota in Wild and Domesticated Barley (2015, methodology): “We then assembled the filtered reads of each sample independently using SOAPdenovo (Heger and Holm, 2000; Experimental Procedures).”