CRISPRseek specifications

Information


Unique identifier OMICS_08507
Name CRISPRseek
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.20.0
Stability Stable
Requirements
parallel, BiocGenerics, IRanges, Biostrings, BiocStyle, BiocParallel, BSgenome, BSgenome.Hsapiens.UCSC.hg19, RUnit, S4Vectors(>=0.9.25), data.table, org.Hs.eg.db, seqinr, TxDb.Hsapiens.UCSC.hg19.knownGene, R(>=3.0.1), hash
Maintained Yes

Versioning


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Documentation


Maintainers


  • person_outline Michael H. Brodsky <>
  • person_outline Lihua Julie Zhu <>

Publication for CRISPRseek

CRISPRseek in publications

 (5)
PMCID: 5856518
PMID: 29453277
DOI: 10.1073/pnas.1713689115

[…] regions within the mouse serpina1 paralogs. crispr/cas9 target sites present in all isoforms and with low predicted off-target activity were identified using the bioconductor software package crisprseek (). four crispr/cas9 target sequences were selected that are conserved in each of the mouse serpina paralogs., aat levels in serum samples were quantified by direct elisa as described (). […]

PMCID: 5423356
PMID: 26829318
DOI: 10.1038/nbt.3471

[…] using chippeakanno. regions spanning each peak start and end (± 50 bp) were searched for sequence elements that were complementary to the nuclease target site with ngg, nga or nag pams using crisprseek,. only peaks that harbor a sequence with less than 7 mismatches to the target site were considered potential off-target sites. these regions are reported in with the number of unique […]

PMCID: 4661947
PMID: 26612492
DOI: 10.1186/s13059-015-0823-x

[…] target site identification. some tools such as ssfinder [] simply output the complete list of pam sites, leaving the user to dictate subsequent site selection, whereas others such as e-crisp [] and crisprseek [] offer additional criteria to filter or rank the target sites., next to the pam requirement, perhaps the most important consideration for crispr modifications is the position of the cut […]

PMCID: 4679368
PMID: 26480473
DOI: 10.1038/nmeth.3624

[…] the sgrna:dna heteroduplex. in this light, we assessed the general frequency of potential off-target sites with three or fewer mismatches for spcas9 guide rnas in exons or promoter regions using crisprseek,. we found that the vast majority of guides (~98% in exons and ~99% in promoters) have one or more off-target sites with 3 or fewer mismatches (), and thus are likely to have some level […]

PMCID: 4460969
PMID: 26060510
DOI: 10.1186/s13073-015-0178-7

[…] road for precision cancer medicine., 1. predict top-ranking single guide rnas (sgrnas) using published tools such as crispr design tool [], sgrna designer [], e-crisp [], via the cas-offinder [] or crisprseek []., 2. clone sgrna into px330 vector [] for transient expression or improved lentivectors [] for stable expression., 3. several groups have reported being able to increase genome-editing […]


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CRISPRseek institution(s)
Program in Gene Function and Expression and Program in Molecular Medicine, University of Massachusetts Medical School, Worcester, MA, USA
CRISPRseek funding source(s)
Supported by the CHDI Foundation, gifts for Huntington’s Disease research at the University of Massachusetts, by the National Institutes of Health (R01GM084361 R01NS38194) and by a National Science Foundation graduate fellowship.

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