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COSMID specifications


Unique identifier OMICS_08858
Alternative name CRISPR Off-target Sites with Mismatches, Insertions, and Deletions
Interface Web user interface
Restrictions to use None
Input data A DNA sequence, PAM suffix
Output data Potential off-target sites corresponding to allowed mismatches and indels, the PAM sequence, the chromosomal location of the hits, and primer designs for experimental validation of the off-target sites.
Computer skills Basic
Stability Stable
Maintained Yes



  • person_outline Gang Bao

Publication for CRISPR Off-target Sites with Mismatches, Insertions, and Deletions

COSMID citations


Generation of App knock in mice reveals deletion mutations protective against Alzheimer’s disease like pathology

Nat Commun
PMCID: 5935712
PMID: 29728560
DOI: 10.1038/s41467-018-04238-0

[…] Potential off-target sites with up to 3 bp mismatches were identified in silico using COSMID. Target fragments on the off-target site were amplified using specific primer sets (Supplementary Table ), and then sequencing analyses were carried out to detect mutations. […]


Validating the concept of mutational signatures with isogenic cell models

Nat Commun
PMCID: 5931590
PMID: 29717121
DOI: 10.1038/s41467-018-04052-8

[…] rtion or deletions, and none were identified. Proliferation rates were also determined for each knockout cell line (Supplementary Fig. ). Moreover, potential off-target sites were also searched using COSMID (, a web-based tool to identify and validate CRISPR/CAS9 off-target sites (see Supplementary Data  for a ranked-list of potential off-target sites of the relevant g […]


Editing out five Serpina1 paralogs to create a mouse model of genetic emphysema

Proc Natl Acad Sci U S A
PMCID: 5856518
PMID: 29453277
DOI: 10.1073/pnas.1713689115

[…] cess and circadian rhythm for line A7 (), and rhythmic process and circadian rhythm for line 24B ().Off-targets for all four gRNAs were predicted using two independent algorithms: Cas OFFinder () and COSMID (), and all results were compiled in Datasets S5 and S6. Results from these predictions were cross-referenced with the list of dysregulated genes (Datasets S2 and S3). No predicted off-target g […]


ssAAVs containing cassettes encoding SaCas9 and guides targeting hepatitis B virus inactivate replication of the virus in cultured cells

Sci Rep
PMCID: 5547162
PMID: 28785016
DOI: 10.1038/s41598-017-07642-6

[…] nline tool. Ten sites were predicted as being the most likely sequences where unintended action of SaCas9-sgRNA-8 would occur. The top three sites were verified by additional predictive tools, namely COSMID and Cas-Offinder tools (Supp. Fig. ). After transfection of HEK293T cells with plasmids encoding SaCas9 and the sgRNA-8 cassette, the T7E1 assay failed to detect indels at the identified off-ta […]


A novel humanized mouse lacking murine P450 oxidoreductase for studying human drug metabolism

Nat Commun
PMCID: 5489481
PMID: 28659616
DOI: 10.1038/s41467-017-00049-x

[…] Six gRNA sequences targeting critical exons of the Rag2, Il2rg, or Fah gene were selected (Fig. , Supplementary Figs  and ) using two different online tools ( and COSMID). Complementary oligonucleotides were annealed and ligated into the DR274 vector (Addgene plasmid # 42250) using standard molecular cloning techniques with the restriction enzyme BsaI (NEB) and […]


Culture time of vitrified/warmed zygotes before microinjection affects the production efficiency of CRISPR Cas9 mediated knock in mice

PMCID: 5450330
PMID: 28396487
DOI: 10.1242/bio.025122

[…] Candidate off-target sites for the gRNAs used for PITCh knock-in were selected using COSMID (, according to a previous protocol (). Genomic regions flanking the top five potential off-target sites were amplified by PCR from knock-in founders using KOD FX […]


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COSMID institution(s)
Department of Biomedical Engineering, Georgia Institute of Technology and Emory University, Atlanta, GA, USA

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