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PhytoCRISP-Ex: a web-based and stand-alone application to find specific target sequences for CRISPR/CAS editing
- Source :
- BMC Bioinformatics, BMC Bioinformatics, BioMed Central, 2016, 17 (1), pp.261. ⟨10.1186/s12859-016-1143-1⟩, BMC Bioinformatics, 2016, 17 (1), pp.261. ⟨10.1186/s12859-016-1143-1⟩
- Publication Year :
- 2016
- Publisher :
- HAL CCSD, 2016.
-
Abstract
- Background With the emerging interest in phytoplankton research, the need to establish genetic tools for the functional characterization of genes is indispensable. The CRISPR/Cas9 system is now well recognized as an efficient and accurate reverse genetic tool for genome editing. Several computational tools have been published allowing researchers to find candidate target sequences for the engineering of the CRISPR vectors, while searching possible off-targets for the predicted candidates. These tools provide built-in genome databases of common model organisms that are used for CRISPR target prediction. Although their predictions are highly sensitive, the applicability to non-model genomes, most notably protists, makes their design inadequate. This motivated us to design a new CRISPR target finding tool, PhytoCRISP-Ex. Our software offers CRIPSR target predictions using an extended list of phytoplankton genomes and also delivers a user-friendly standalone application that can be used for any genome. Results The software attempts to integrate, for the first time, most available phytoplankton genomes information and provide a web-based platform for Cas9 target prediction within them with high sensitivity. By offering a standalone version, PhytoCRISP-Ex maintains an independence to be used with any organism and widens its applicability in high throughput pipelines. PhytoCRISP-Ex out pars all the existing tools by computing the availability of restriction sites over the most probable Cas9 cleavage sites, which can be ideal for mutant screens. Conclusions PhytoCRISP-Ex is a simple, fast and accurate web interface with 13 pre-indexed and presently updating phytoplankton genomes. The software was also designed as a UNIX-based standalone application that allows the user to search for target sequences in the genomes of a variety of other species. Electronic supplementary material The online version of this article (doi:10.1186/s12859-016-1143-1) contains supplementary material, which is available to authorized users.
- Subjects :
- 0301 basic medicine
Eukaryotes
ved/biology.organism_classification_rank.species
Computational biology
Biology
Biochemistry
Genome
03 medical and health sciences
Genome editing
Structural Biology
[SDV.BBM] Life Sciences [q-bio]/Biochemistry, Molecular Biology
Humans
CRISPR
Web application
[SDV.BBM]Life Sciences [q-bio]/Biochemistry, Molecular Biology
Model organism
Cas9
Molecular Biology
Genetics
Internet
[SDV.BIBS] Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
030102 biochemistry & molecular biology
Genome, Human
ved/biology
business.industry
Applied Mathematics
Protists
[SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM]
Computer Science Applications
030104 developmental biology
Human genome
CRISPR-Cas Systems
DNA microarray
business
Software
Subjects
Details
- Language :
- English
- ISSN :
- 14712105
- Database :
- OpenAIRE
- Journal :
- BMC Bioinformatics, BMC Bioinformatics, BioMed Central, 2016, 17 (1), pp.261. ⟨10.1186/s12859-016-1143-1⟩, BMC Bioinformatics, 2016, 17 (1), pp.261. ⟨10.1186/s12859-016-1143-1⟩
- Accession number :
- edsair.doi.dedup.....5336e37dd2ddc2c0b9fbdc66b41421aa