Please cite the paper below for the CRISPRseek package.

Zhu LJ, Holmes BR, Aronin N, Brodsky MH (2014) CRISPRseek: A Bioconductor Package to Identify Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing Systems. PLoS ONE 9(9): e108424.<doi:10.1371/journal.pone.0108424>

Lihua Julie Zhu (2015). Overview of guide RNA design tools for CRISPR-Cas9 genome editing technology. Front. Biol., 10(4): 289-296

Corresponding BibTeX entries:

  @Article{,
    title = {CRISPRseek: A Bioconductor Package to Identify
      Target-Specific Guide RNAs for CRISPR-Cas9 Genome-Editing
      Systems},
    author = {Lihua Julie Zhu and Benjamin R. Holmes and Neil Aronin
      and Michael H. Brodsky},
    journal = {PLoS one},
    volume = {9},
    year = {2014},
    number = {9},
    url = {http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4172692/},
    pubmedid = {PMC4172692},
    abstract = {CRISPR-Cas systems are a diverse family of RNA-protein
      complexes in bacteria that target foreign DNA sequences for
      cleavage. Derivatives of these complexes have been engineered to
      cleave specific target sequences depending on the sequence of a
      CRISPR-derived guide RNA (gRNA) and the source of the Cas9
      protein. Important considerations for the design of gRNAs are to
      maximize aimed activity at the desired target site while
      minimizing off-target cleavage. Because of the rapid advances in
      the understanding of existing CRISPR-Cas9-derived RNA-guided
      nucleases and the development of novel RNA-guided nuclease
      systems, it is critical to have computational tools that can
      accommodate a wide range of different parameters for the design
      of target-specific RNA-guided nuclease systems. We have developed
      CRISPRseek, a highly flexible, open source software package to
      identify gRNAs that target a given input sequence while
      minimizing off-target cleavage at other sites within any selected
      genome. CRISPRseek will identify potential gRNAs that target a
      sequence of interest for CRISPR-Cas9 systems from different
      bacterial species and generate a cleavage score for potential
      off-target sequences utilizing published or user-supplied weight
      matrices with position-specific mismatch penalty scores.
      Identified gRNAs may be further filtered to only include those
      that occur in paired orientations for increased specificity
      and/or those that overlap restriction enzyme sites. For
      applications where gRNAs are desired to discriminate between two
      related sequences, CRISPRseek can rank gRNAs based on the
      difference between predicted cleavage scores in each input
      sequence. CRISPRseek is implemented as a Bioconductor package
      within the R statistical programming environment, allowing it to
      be incorporated into computational pipelines to automate the
      design of gRNAs for target sequences identified in a wide variety
      of genome-wide analyses. CRISPRseek is available under the GNU
      General Public Licence v3.0 at http://www.bioconductor.org.},
  }

  @Article{,
    title = {Overview of guide RNA design tools for CRISPR-Cas9 genome
      editing technology},
    author = {Lihua Julie Zhu},
    journal = {Front. Biol.},
    volume = {10},
    year = {2015},
    number = {4},
    abstract = {CRISPR-Cas (Clustered, Regularly Interspaced, Short
      Palindromic Repeats CRISPR-associated (Cas)) RNA guided
      endonuclease has emerged as the most effective and widely used
      genome editing technology, which has become the most exciting and
      rapidly advancing research field. Efficient genome editing by the
      CRISPR-Cas9 system has been demonstrated in many species, and
      several labs have established CRISPR-Cas9 as a screening tool for
      systematic genetic analysis, similar to shRNA screening.  At
      least three companies have been founded to leverage this
      technology for therapeutic uses. To facilitate the implementation
      of this technology, many software tools have been developed to
      identify guide RNAs that effectively target a desired genomic
      region. Here, I provide an overview of the technology, focusing
      on guide RNA design principles, available software tools and
      their strengths and weaknesses.},
  }