We are analyzing https://link.springer.com/article/10.1186/s13062-015-0035-z.

Title:
“Off-Spotter”: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs | Biology Direct
Description:
Background CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated nucleases) is a powerful component of the prokaryotic immune system that has been adapted for targeted genetic engineering in higher organisms. A key element of CRISPR/Cas is the “guide” RNA (gRNA) that is ~20 nucleotides (nts) in length and designed to be complementary to the intended target site. An integral requirement of the CRISPR/Cas system is that the target site be followed by a protospacer adjacent motif (PAM). Care needs to be exercised during gRNA design to avoid unintended (“off-target”) interactions. Results We designed and implemented the Off-Spotter algorithm to assist with the design of optimal gRNAs. When presented with a candidate gRNA sequence and a PAM, Off-Spotter quickly and exhaustively identifies all genomic sites that satisfy the PAM constraint and are identical or nearly-identical to the provided gRNA. Off-Spotter achieves its extreme performance through purely algorithmic means and not through hardware accelerators such as graphical processing units (GPUs). Off-Spotter also allows the user to identify on-the-fly how many and which nucleotides of the gRNA comprise the “seed”. Off-Spotter’s output includes a histogram showing the number of potential off-targets as a function of the number of mismatches. The output also includes for each potential off-target the site’s genomic location, a human genome browser hyperlink to the corresponding location, genomic annotation in the vicinity of the off-target, GC content, etc. Conclusion Off-Spotter is very fast and flexible and can help in the design of optimal gRNAs by providing several PAM choices, a run-time definition of the seed and of the allowed number of mismatches, and a flexible output interface that allows sorting of the results, optional viewing/hiding of columns, etc. A key element of Off-Spotter is that it does not have a rigid definition of the seed: instead, the user can declare both the seed’s location and extent on-the-fly. We expect that this flexibility in combination with Off-Spotter’s speed and richly annotated output will enable experimenters to interactively and quickly explore different scenarios and gRNA possibilities. Reviewed This article was reviewed by Dr Eugene Koonin and Dr Frank Eisenhaber.
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Keywords {🔍}

pubmed, offspotter, article, cas, pam, google, scholar, offtargets, sequence, grna, offtarget, table, number, crisprcas, potential, genomic, genome, sites, information, user, central, seed, system, nucleotides, tools, location, crispr, mismatches, additional, mer, guide, results, annotation, grnas, figure, mers, rigoutsos, target, report, algorithm, chromosome, make, rna, query, problem, string, stage, cell, file, authors,

Topics {✒️}

crispr-cas9 genome-editing systems cas9 rna-guided endonucleases crispr-cas9-mediated gene inactivation engineered crispr-cas systems crispr/cas nuclease system begin{array}{cc}\hfill \left crispr/cas systems significantly outperforms cas-offinder open access license crispr-mediated genome engineering cas nuclease genes specific crispr editing truncated guide rnas isidore rigoutsos rna-guided complex rna-directed adaptive immunity crispr endonuclease cas9 designing crispr sgrna abbreviation “crispr/cas” crispr/cas abbreviation abbreviations crispr/cas targeted genetic engineering crispr/cas system crispr/cas system [4-6] protospacer adjacent motif user-provided query n1n2n3…n15n16 mobile genetic elements crispr-cas9 system crispr/cas9 system article download pdf www server access crispr-cas site crispr/cas site microrna target prediction article pliatsika molecular biology detail 16-nucleotide string n1n2n3…n15n16 candidate guide rna target cleavage sites privacy choices/manage cookies author information authors full size image genome editing genomic 20-mers n1n2n3…n15n16 gpu-based software solution cas-offinder report short rnas current implementation incorporates distinct 20-mers aactcctgacctcaga-nnnn crispr/cas

Questions {❓}

How does the competition fare in this respect and can this functionality be put on top of the existing Off-Spotter?
Short RNAs: how big is this iceberg?

Schema {🗺️}

WebPage:
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         description:CRISPR/Cas (Clustered Regularly Interspaced Short Palindromic Repeats/CRISPR associated nucleases) is a powerful component of the prokaryotic immune system that has been adapted for targeted genetic engineering in higher organisms. A key element of CRISPR/Cas is the “guide” RNA (gRNA) that is ~20 nucleotides (nts) in length and designed to be complementary to the intended target site. An integral requirement of the CRISPR/Cas system is that the target site be followed by a protospacer adjacent motif (PAM). Care needs to be exercised during gRNA design to avoid unintended (“off-target”) interactions. We designed and implemented the Off-Spotter algorithm to assist with the design of optimal gRNAs. When presented with a candidate gRNA sequence and a PAM, Off-Spotter quickly and exhaustively identifies all genomic sites that satisfy the PAM constraint and are identical or nearly-identical to the provided gRNA. Off-Spotter achieves its extreme performance through purely algorithmic means and not through hardware accelerators such as graphical processing units (GPUs). Off-Spotter also allows the user to identify on-the-fly how many and which nucleotides of the gRNA comprise the “seed”. Off-Spotter’s output includes a histogram showing the number of potential off-targets as a function of the number of mismatches. The output also includes for each potential off-target the site’s genomic location, a human genome browser hyperlink to the corresponding location, genomic annotation in the vicinity of the off-target, GC content, etc. Off-Spotter is very fast and flexible and can help in the design of optimal gRNAs by providing several PAM choices, a run-time definition of the seed and of the allowed number of mismatches, and a flexible output interface that allows sorting of the results, optional viewing/hiding of columns, etc. A key element of Off-Spotter is that it does not have a rigid definition of the seed: instead, the user can declare both the seed’s location and extent on-the-fly. We expect that this flexibility in combination with Off-Spotter’s speed and richly annotated output will enable experimenters to interactively and quickly explore different scenarios and gRNA possibilities. This article was reviewed by Dr Eugene Koonin and Dr Frank Eisenhaber.
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         Off-targets
         Cas endonucleases
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         Guide RNAs
         gRNAs
         Indexing
         Hashing
         Life Sciences
         general
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