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Results for « CRISPR »

Allows quantification and visualization of CRISPR-Cas9 outcomes, as well as evaluation of effects on coding sequences, noncoding elements and selected off-target sites. CRISPResso is a suite of computational tools that offers several features, including batch sample analysis via command line interface, integration with other pipelines, tunable parameters of sequence quality and alignment fidelity, discrete measurement of insertions, deletions, and nucleotide substitutions, and distinction between non-homologous end joining (NHEJ), homology-directed repair (HDR), and mixed mutation events.
Resolves and localizes individual mutant alleles with respect to the endonuclease cut site. CrispRVariants quantifies and visualizes individual variant alleles from either traditional Sanger sequencing or high-throughput CRISPR-Cas9 mutagenesis sequencing experiments. CrispRVariants was designed with interactivity in mind, explicitly allowing users to detect problems and filter sequences appropriately before estimating mutation efficiency. This toolkit can be easily used to create a variant allele summary plot and accompanying table of counts. CrispRVariants enables immediate comparison of variant spectra between target locations.
Proposes a set of bioinformatic tools assisting biologists in the development and the setting up of a CRISPR genotyping scheme. In the pre-processing phase, the comparison of CRISPRs is mandatory and may be fulfilled using the CRISPRcomparison tool, which helps in selecting the most appropriate CRISPR loci and associated primers for the PCR amplification. CRISPRcomparison allows the identification of families of strains that share a CRISPR, inside species with high genetic diversity or the identification of homologous CRISPRs within species containing multiple CRISPR loci. In the post-processing phase, the CRISPRtionary program is very interesting since it allows the user to easily compare multiple alleles of a CRISPR locus investigated in a collection of strains and to obtain pre-calculated files that may be directly used in clustering analysis.
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An interface to extract with precision and to further analyse clustered regularly interspaced short palindromic repeats (CRISPRs) from genomic sequences. Four main advantages may be cited: (i) short CRISPR-like structures are detected, they are labelled questionable but may be of great interest if later confirmed; (ii) conserved regions are accurately defined to single base pair resolution; (iii) summary files may be uploaded (CRISPR properties summary and spacers file in Fasta format) and (iv) flanking sequences or spacers can be easily extracted and blasted against different databases.
A simple and functional web server for selecting rational CRISPR/Cas targets from an input sequence. The CRISPR/Cas system is a promising technique for genome engineering which allows target-specific cleavage of genomic DNA guided by Cas9 nuclease in complex with a guide RNA (gRNA), that complementarily binds to a ~20 nt targeted sequence. The target sequence requirements are twofold. First, the 5'-NGG protospacer adjacent motif (PAM) sequence must be located adjacent to the target sequence. Second, the target sequence should be specific within the entire genome in order to avoid off-target editing. CRISPRdirect enables users to easily select rational target sequences with minimized off-target sites by performing exhaustive searches against genomic sequences. The server currently incorporates the genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, C. elegans, Arabidopsis, rice, Sorghum, and budding yeast.
Provides annotation of CRISPR—Cas systems including (i) CRISPR arrays of repeat-spacer units, and cas genes, (ii) type (and subtype) of predicted system(s) and (iii) anti-repeats (part of tracrRNA genes in type II CRISPR–Cas systems). The CRISPRone website also provides online prediction of CRISPR–Cas systems given genomic sequences, using a pipeline with integrated checking of false-CRISPRs. It can be used to submit sequences to the server for prediction, look up pre-calculated CRISPR-Cas systems or check out mock CRISPRs (elements that superficially reassemble CRISPRs).
Predicts the most likely targets of CRISPR RNAs. This can be used to discover targets in newly sequenced genomic or metagenomic data. The inputs into CRISPRTarget are predicted CRISPR arrays or spacer sequences. The output provided is either visual in HTML format, but can also be saved as text and opened in a spreadsheet. The target sequence is typically displayed as an R-loop, depicting a specified part of the crRNA, as well as both the target and non-target strand of the double-stranded target DNA. The target sequence R-loop can be fully reverse complemented, when users suspect that the direction of transcription of the CRISPR array starts from the downstream end instead.
A central hub of CRISPR/Cas-based genome editing. Presently, this database holds a total of 4680 entries of 223 unique genes from 32 model and other organisms. It encompasses information about the organism, gene, target gene sequences, genetic modification, modifications length, genome editing efficiency, cell line, assay, etc. This depository is developed using the open source LAMP (Linux Apache MYSQL PHP) server. User-friendly browsing, searching facility is integrated for easy data retrieval. It also includes useful tools like BLAST CrisprGE, BLAST NTdb and CRISPR Mapper.
A highly flexible, open source software package to identify gRNAs that target a given input sequence while minimizing off-target cleavage at other sites within any selected genome. CRISPRseek will identify potential gRNAs that target a sequence of interest for CRISPR-Cas9 systems from different bacterial species and generate a cleavage score for potential off-target sequences utilizing published or user-supplied weight matrices with position-specific mismatch penalty scores. Identified gRNAs may be further filtered to only include those that occur in paired orientations for increased specificity and/or those that overlap restriction enzyme sites.
Permits users to predict on-target activity of in-silico sgRNAs efficiently based on the applications of Support Vector Machine (SVM) model. This tool provides two key factors that improve the in-silico prediction of single-guide RNA (sgRNA) activity in CRISPR/Cas9 system. In first, all possible single, di-nucleotides, tri-nucleotides and tetra-nucleotides position specific features and position independent features are incorporates. Secondly, active sgRNA is enriched with “A” but is “T” depleted.
A web-based and command line tool, that enables accurate identification of CRISPR arrays in genomes, their direction, repeat spacer boundaries, substitutions, insertions or deletions in repeats and spacers and lists cas genes that are annotated in the genome. This data is combined into a searchable database, CRISPRBank, currently version 1.0. Spacer outputs from CRISPRDetect can then be directly used to search for targets in viral and other sequence databases using the linked tool, CRISPRTarget. CRISPRDetect enables more accurate detection of arrays and spacers and its gff output is suitable for inclusion in genome annotation pipelines and visualisation. It has been used to analyse all complete bacterial and archaeal reference genomes.
Serves for the processing of pooled genome-wide. CRISPRcleanR allows users to identify biased genomic regions from CRISPR-KO screen datasets. It also corrects both read count and log fold change (logFC) of individual single guide RNA (sgRNA) in such regions. It can be used for reducing false positive calls while keeping the true positive rate of known essential genes largely unchanged. Moreover, it assists in detecting essential genes, even within focally amplified regions.
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Results for « CRISPR »

A database of CRISPR/Cas9 target sequences that have been experimentally validated in zebrafish. CRISPRz can be searched using multiple inputs such as ZFIN IDs, accession number, UniGene ID, or gene symbols from zebrafish, human and mouse. CRISPRz was developed in an effort to provide a comprehensive list of validated CRISPR targets from published sources as well as from an ongoing genome-wide knockout project in the zebrafish genome. Data will be added as more validated CRISPR targets are published or contributed from unpublished, in-house projects. The database is also open for data submission from the research community.
Utilizes the CRISPRFinder program to identify putative CRISPRs and additional tests to further screen for the smallest CRISPRs in a polyphasic approach. Indeed the CRISPRFinder program is conceived to authorize the largest number of possible CRISPRs, especially the shortest ones, containing one or two spacers. The main idea of the program is to first find possible CRISPR localizations in a genomic sequence and then check if these regions contain a cluster that possess the characteristics of "obvious" CRISPR, i.e. containing at least three repeats.
IMG/M / Integrated Microbial Genomes with Microbiome Samples
A database for analysis and annotation of genome and metagenome datasets in a comprehensive comparative context. IMG/M includes archaea, bacteria, eukarya, plasmids, viruses, genome fragments (partially sequenced genomes), as well as metagenomes and metatranscriptome datasets. IMG performs feature prediction including identification of protein-coding genes, non-coding RNAs and regulatory RNA features, as well as CRISPR elements.
WGE / Wellcome Trust Sanger Institute Genome Editing database
Uses methods to compute, visualize and select optimal CRISPR sites in a genome browser environment. The WGE database currently stores single and paired CRISPR sites and pre-calculated off-target information for CRISPRs located in the mouse and human exomes. Scoring and display of off-target sites is simple, and intuitive, and filters can be applied to identify high-quality CRISPR sites rapidly. WGE also provides a tool for the design and display of gene targeting vectors in the same genome browser, along with gene models, protein translation and variation tracks.
Facilitates the use of the CRISPR/Cas9 system as a genome editing tool for functional studies and molecular breeding of grapes. Among other functions, the Grape-CRISPR database allows users to identify and select multi-protospacers for editing similar sequences in grape genomes simultaneously. The database contains two main sections: Search and Design. In the Search section, users can identify appropriate protospacer and protospacer-adjacent motif (PAM) sites of a gene by providing certain inquiry information such as locus location, gene ID or Pfam ID. The Design section is for protospacer design. Users can detect and design protospacers and PAMs in the sequences of interest by using the Perl scripts provided.
SEA / Super-Enhancer Archive
Focuses on integrating experimentally and computationally identified super-enhancers and annotating their potential roles in the regulation of cell identity gene expression in a cell type-specific manner. The current release of SEA incorporates 83 996 super-enhancers computationally or experimentally identified in 134 cell types/tissues/diseases, including human (75 439, three of which were experimentally identified), mouse (5879, five of which were experimentally identified), Drosophila melanogaster (1774) and Caenorhabditis elegans (904). To facilitate data extraction, SEA supports multiple search options, including species, genome location, gene name, cell type/tissue and super-enhancer name. The response provides detailed (epi)genetic information, incorporating cell type specificity, nearby genes, transcriptional factor binding sites, CRISPR/Cas9 target sites, evolutionary conservation, SNPs, H3K27ac, DNA methylation, gene expression and TF ChIP-seq data. Moreover, analytical tools and a genome browser were developed for users to explore super-enhancers and their roles in defining cell identity and disease processes in depth.
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Results for « CRISPR »

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