CRISPRloci: comprehensive and accurate annotation of CRISPR–Cas systems

CRISPRcasIdentifier: Machine learning for accurate identification and classification of CRISPR-Cas systems

(2020) Victor A Padilha et al.   GigaScience

CRISPRidentify: identification of CRISPR arrays using machine learning approach

(2020) Alexander Mitrofanov et al.   NUCLEIC ACIDS RESEARCH

CRISPR-Cas bioinformatics

(2019) Omer S. Alkhnbashi et al.   METHODS

Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants

(2019) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

Bioconda: sustainable and comprehensive software distribution for the life sciences

(2018) Björn Grüning et al.   NATURE METHODS

Freiburg RNA tools: a central online resource for RNA-focused research and teaching

(2018) Martin Raden et al.   NUCLEIC ACIDS RESEARCH

CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins

(2018) David Couvin et al.   NUCLEIC ACIDS RESEARCH

Comprehensive search for accessory proteins encoded with archaeal and bacterial type III CRISPR-cas gene cassettes reveals 39 new cas gene families

(2018) Shiraz A. Shah et al.   RNA Biology

Characterizing leader sequences of CRISPR loci

(2016) Omer S. Alkhnbashi et al.   BIOINFORMATICS

Structural constraints and enzymatic promiscuity in the Cas6-dependent generation of crRNAs

(2016) Viktoria Reimann et al.   NUCLEIC ACIDS RESEARCH

An updated evolutionary classification of CRISPR–Cas systems

(2015) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

CRISPRstrand: predicting repeat orientations to determine the crRNA-encoding strand at CRISPR loci

(2014) Omer S. Alkhnbashi et al.   BIOINFORMATICS

CRISPR adaptive immune systems of Archaea

(2014) Gisle Vestergaard et al.   RNA Biology

CRISPRmap: an automated classification of repeat conservation in prokaryotic adaptive immune systems

(2013) Sita J. Lange et al.   NUCLEIC ACIDS RESEARCH

Protospacer recognition motifs

(2013) Shiraz A. Shah et al.   RNA Biology

RNA Accessibility in cubic time

(2011) Stephan H Bernhart et al.   Algorithms for Molecular Biology

ViennaRNA Package 2.0

(2011) Ronny Lorenz et al.   Algorithms for Molecular Biology

HHblits: lightning-fast iterative protein sequence searching by HMM-HMM alignment

(2011) Michael Remmert et al.   NATURE METHODS

Evolution and classification of the CRISPR–Cas systems

(2011) Kira S. Makarova et al.   NATURE REVIEWS MICROBIOLOGY

CRISPR/Cas and Cmr modules, mobility and evolution of adaptive immune systems

(2010) Shiraz A. Shah et al.   RESEARCH IN MICROBIOLOGY