title: [Bioinformatics Analysis of Clustered Regularly Interspaced Short Palindromic Repeats in the Genomes of Shigella].
abstract: This study was aimed to explore the features of clustered regularly interspaced short palindromic repeats (CRISPR) structures in Shigella by using bioinformatics. We used bioinformatics methods, including BLAST, alignment and RNA structure prediction, to analyze the CRISPR structures of Shigella genomes. The results showed that the CRISPRs existed in the four groups of Shigella, and the flanking sequences of upstream CRISPRs could be classified into the same group with those of the downstream. We also found some relatively conserved palindromic motifs in the leader sequences. Repeat sequences had the same group with corresponding flanking sequences, and could be classified into two different types by their RNA secondary structures, which contain "stem" and "ring". Some spacers were found to homologize with part sequences of plasmids or phages. The study indicated that there were correlations between repeat sequences and flanking sequences, and the repeats might act as a kind of recognition mechanism to mediate the interaction between foreign genetic elements and Cas proteins.
authors.forename: Pengfei
authors.initials: P
authors.lastname: Wang
authors.forename: Yingfang
authors.initials: Y
authors.lastname: Wang
authors.forename: Guangcai
authors.initials: G
authors.lastname: Duan
authors.forename: Zerun
authors.initials: Z
authors.lastname: Xue
authors.forename: Linlin
authors.initials: L
authors.lastname: Wang
authors.forename: Xiangjiao
authors.initials: X
authors.lastname: Guo
authors.forename: Haiyan
authors.initials: H
authors.lastname: Yang
authors.forename: Yuanlin
authors.initials: Y
authors.lastname: Xi
mesh_terms: D001483:Base Sequence; D064112:Clustered Regularly Interspaced Short Palindromic Repeats; D019295:Computational Biology; D016680:Genome, Bacterial; D010957:Plasmids; D012760:Shigella / Q000235:genetics*