CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci. - Omer S. Alkhnbashi; Fabrizio Costa; Shiraz A. Shah; Roger A. Garrett; Sita J. Saunders; Rolf Backofen (Bioinform., 2014)

Characterizing leader sequences of CRISPR loci. - Omer S. Alkhnbashi; Shiraz A. Shah; Roger A. Garrett; Sita J. Saunders; Fabrizio Costa; Rolf Backofen (Bioinform., 2016)

Casboundary: automated definition of integral Cas cassettes. - Victor Alexandre Padilha; Omer S. Alkhnbashi; Van Dinh Tran; Shiraz A. Shah; André C. P. L. F. de Carvalho; Rolf Backofen (Bioinform., 2021)

CRISPRloci: comprehensive and accurate annotation of CRISPR-Cas systems. - Omer S. Alkhnbashi; Alexander Mitrofanov; Robson Bonidia; Martin Raden; Van Dinh Tran; Florian Eggenhofer; Shiraz A. Shah; Ekrem Öztürk; Victor Alexandre Padilha; Danilo Sipoli Sanches; André C. P. L. F. de Carvalho; Rolf Backofen (Nucleic Acids Res., 2021)