sgRNA Scorer specifications

Information


Unique identifier OMICS_15503
Name sgRNA Scorer
Interface Web user interface
Restrictions to use None
Input data The genomic sequence, user's email address, the CRISPR system, the spacer length, the PAM sequence and orientation.
Input format FASTA
Output data The guide RNA sequences and scores.
Programming languages Python
Computer skills Basic
Version 2.0
Stability Stable
Maintained Yes

Documentation


Maintainer


  • person_outline Raj Chari <>

Information


Unique identifier OMICS_15503
Name sgRNA Scorer
Software type Application/Script
Interface Command line interface
Restrictions to use None
Input data The genomic sequence.
Input format FASTA
Output data The guide RNA sequences and scores.
Operating system Unix/Linux, Mac OS
Programming languages Python
Computer skills Advanced
Version 2.0
Stability Stable
Requirements
BioPython, Sci-kit learn
Maintained Yes

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Documentation


Maintainer


  • person_outline Raj Chari <>

Publication for sgRNA Scorer

sgRNA Scorer in publications

 (4)
PMCID: 5814880
PMID: 29267886
DOI: 10.1093/nar/gkx1268

[…] between the two algorithms (rule set i and ii) illustrated the different predicted activities they assigned to our sgrnas ()., we next tested the alternative library-on-library approach, sgrna scorer by chari et al. (), on our dataset. the correlation between our data and the predicted activities from this algorithm did not improve compared to rule set ii (), although a trend of high […]

PMCID: 5517805
PMID: 28724437
DOI: 10.1186/s12943-017-0692-x

[…] element [] to remove an internal bbsi restriction site. the 20-nt grna sequences flanking a 3.1–3.8 kb region (encompassing the first two exons) of mouse casc15 (2610307p16rik) were designed using sgrna scorer with casfinder []. detailed methods are available upon request., lentivirus and mscv-based retroviral vectors were produced to generate knockdown and overexpression constructs […]

PMCID: 5024423
PMID: 27630115
DOI: 10.1186/s13062-016-0147-0

[…] employing any prior knowledge of the sequence specificities of the nucleases. this was not the case for spcas9, where we exploited the existence of grna prediction tools: sgrna designer [] and sgrna scorer 1.0 [] and accepted targets scoring above either 0.5 or 50, respectively. in case of cpf1 nucleases, representative targets were picked from the 20 targets used on fig. . all targets […]

PMCID: 4786925
PMID: 26750397
DOI: 10.1038/mt.2016.1

[…] however, although the algorithm was validated with a previous crispr knockout library screen in human and mouse cells, it was not tested for designing a grna for a given input sequence. similarly, sgrna scorer () ranks grnas for high activity based on an algorithm generated using data from grnas tested in hek293t cells. this study noted some correlation between site accessibility and grna […]


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sgRNA Scorer institution(s)
Department of Genetics, Harvard Medical School, Boston, MA, USA; Wyss Institute for Biologically Inspired Engineering, Harvard University, Cambridge, MA, USA
sgRNA Scorer funding source(s)
This work was supported by NIH grant P50 HG005550.

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