@Article{Lange_Alkhnbashi_Rose-CRISP_autom_class-NAR2013,
  author =	 {Lange, Sita J. and Alkhnbashi, Omer S. and Rose, Dominic 
                  and Will, Sebastian and Backofen, Rolf},
  title =	 {{CRISPRmap}: an automated classification of repeat 
                  conservation in prokaryotic adaptive immune systems},
  journal =	 NAR,
  year =	 {2013},
  volume =	 {41},
  number =	 {17},
  pages =	 {8034-44},
  user =	 {sita},
  pmid =	 {23863837},
  doi = 	 {10.1093/nar/gkt606},
    note = 	 {SJL, OSA and DR contributed equally to this work.},
  issn = 	 {0305-1048},
  issn = 	 {1362-4962},
  abstract =	 {Central to Clustered Regularly Interspaced Short 
                  Palindromic Repeat (CRISPR)-Cas systems are repeated RNA 
                  sequences that serve as Cas-protein-binding templates. 
                  Classification is based on the architectural composition of 
                  associated Cas proteins, considering repeat evolution is 
                  essential to complete the picture. We compiled the largest 
                  data set of CRISPRs to date, performed comprehensive, 
                  independent clustering analyses and identified a novel set 
                  of 40 conserved sequence families and 33 potential structure 
                  motifs for Cas-endoribonucleases with some distinct 
                  conservation patterns. Evolutionary relationships are 
                  presented as a hierarchical map of sequence and structure 
                  similarities for both a quick and detailed insight into the 
                  diversity of CRISPR-Cas systems. In a comparison with 
                  Cas-subtypes, I-C, I-E, I-F and type II were strongly 
                  coupled and the remaining type I and type III subtypes were 
                  loosely coupled to repeat and Cas1 evolution, respectively. 
                  Subtypes with a strong link to CRISPR evolution were almost 
                  exclusive to bacteria; nevertheless, we identified rare 
                  examples of potential horizontal transfer of I-C and I-E 
                  systems into archaeal organisms. Our easy-to-use web server 
                  provides an automated assignment of newly sequenced CRISPRs 
                  to our classification system and enables more informed 
                  choices on future hypotheses in CRISPR-Cas research: 
                  http://rna.informatik.uni-freiburg.de/CRISPRmap.}
}