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CRISPR design
A web tool crafted to simplify the process of CRISPR guide selection in an input DNA sequence by (i) discovering possible offtargets genome-wide, (ii) highlighting guides with high target specificity, and (iii) flagging guides with numerous or genic offtargets in target genomes. The CRISPR design tool allows users to enter a 23-1000bp DNA sequence of interest and will find all SpCas9 target sites within the input sequence. The result will contain a rank ordered list of target sites based on predicted specificity.
ProtospacerWB / Protospacer Workbench
An offline software application for rapid, flexible design of Cas9 sgRNA in one or more target sites, for any CRISPR application in any organism where a full or at least partial reference assembly is available. ProtospacerWB was born from the need to transfer CRISPR technology to new research communities. The main goals of the software tool are:(i) Be intuitive enough for users without programming knowledge, (ii) Be powerful enough for advanced experimental designs, (iii) Operate on any FASTA sequence no matter the size, type or quality (eg. reference genome, partial assembly, short fragments), (iv) Create and share guide-RNA design libraries, (v) Inform the user of potential off-target sites, (vi) Rank most likely off-target sites, (vii)Provide statistical reports for any design.
Allows for the design of CRISPR guide RNA libraries that can be used to edit coding and noncoding genomic regions. GuideScan produces high-density sets of guide RNAs (gRNAs) for single- and paired-gRNA genome-wide screens. Rather than using an alignment tool, GuideScan uses a retrieval tree (trie) data structure, which efficiently and precisely enumerates all targetable sequences present in a given genome. Traversals of the trie allow for the computation of sequence mismatch neighborhoods, which are used to construct databases of gRNAs whose target sites are unique in the genome up to a user-defined number of mismatches. The GuideScan website allows users to input coordinates of genomic features in batch, to choose between designing single internal gRNAs or pairs of flanking gRNAs, and retrieve for each genomic coordinate a pre-defined number of gRNAs or gRNA pairs.
sgRNA Scorer
Allows users to identify single guide RNA (sgRNA) sites for any protospacer adjacent motif (PAM) sequence of interest. sgRNA Scorer predictions has been validated in human cells across multiple CRISPR/Cas9 systems. Given an input sequence or list of sequences as well as a CRISPR system with a defined spacer length and PAM sequence, this interactive web tool will identify putative sites and assign a predicted activity based on a support vector machine model. This software is available online or can be used locally as a standalone program.
A user-friendly program to aid researchers in choosing appropriate target sites in a gene of interest for type II CRISPR/Cas-derived RNA-guided endonucleases (RGENs), which are now widely used for biomedical research and biotechnology. Cas-Designer rapidly provides the list of all possible guide RNA sequences in a given input DNA sequence and their potential off-target sites including bulge-type sites in a genome of choice. In addition, the program assigns an out-of-frame score to each target site to help users choose appropriate sites for gene knockout. Cas-Designer shows the results in an interactive table and provides user-friendly filter functions.
A web tool for CRISPR- and TALEN-based genome editing. The overarching principle of CHOPCHOP is to provide an intuitive and powerful tool that can serve first time as well as experienced users. The basic mode offers optimized defaults for the basic user, while more advanced users can select from a wide range of options curated from the literature by their relevance and utility. All options are presented in a tabulated and organized manner to help users quickly visualize and evaluate options when designing CRISPR experiments.
CLD / CRISPR library designer
Aims to the design of custom single guide RNA (sgRNA) libraries for all organisms with annotated genomes. CLD is suitable for the design of libraries using modified CRISPR enzymes and targeting non-coding regions. This software automates all tasks for the generation of sgRNA libraries. It can design libraries of variable size ranging from a few hundred genes to genome-scale for all annotated genomes available from ENSEMBL. CLD implements the following steps: (i) it downloads and reformats ENSEMBL databases, (ii) predicts and filters sgRNA target sites for a provided list of genes, and (iii) reports the results in a ‘ready-to-order’ library file containing nucleotide sequences for on-chip synthesis and subsequent cloning into target vectors.
Detects putative sgRNA off-targets in CRISPR/Cas applications. BreakingCas allows working with all eukaryotic genomes available in the ENSEMBL database, while other existing tools can only work with a few tens model genomes in the best cases. It provides a user-friendly browser for a detailed inspection of the genomic neighbourhood of every single potential off-target so as to qualitatively assess them. This web server allows specifying the characteristics and parameters of the nuclease to be used, although predefined set are available for several popular Cas proteins.
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.
Identifies potential off-target sites of given Cas9/gRNA targets or target pairs in any user-specified sequence or genome. CasOT is an open-source tool with several tunable parameters like PAM type and the mismatch number in seed and non-seed regions. It offers three searching modes, single-gRNA, paired-gRNA and target-and-off-target. Users can specify several parameters for search, including the allowed level of PAM type (four levels are available), and the maximum number of mismatches allowed in seed region.
CASPER / CRISPR Associated Software for Pathway Engineering and Research
Allows analysis of on and off-target activity in any organism with any Cas enzyme. CASPER is a method that implements flexible algorithms to guide precise genome editing. The software can perform multitargeting analysis in any organism and with any endonuclease desired and an analysis on multiple organisms to identify repeated sequences shared across them. It can be used to identify off-targets and multitargeting analysis for genome editing of a consortium.
CRISPR-ERA / CRISPR-mediated Editing, Repression, and Activation
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A web tool for automated genome wide single guide RNA (sgRNA) design. CRISPR-ERA can provide different sgRNA searching approaches for genome editing, such as Cas9 nuclease. In addition, CRISPR-ERA also generates sgRNAs for gene activation or repression using a large-scale database of CRISPRi in different genomes. Now nine (two bacterial species: E.coli, B. subtilis; one yeast: S. cerevasiae; C. elegans, fruit fly, zebrafish, mouse, rat, human) model organisms are provided in this web tool.
A web application for the design and optimization of guide sequences that target both coding and non-coding regions in spCas9 CRISPR system across human, mouse, zebrafish, fly and worm genomes. CRISPR-DO uses a computational sequence model to predict sgRNA efficiency, and employs a specificity scoring function to evaluate the potential of off-target effect. It also provides information on functional conservation of target sequences, as well as the overlaps with exons, putative regulatory sequences and single nucleotide polymorphisms (SNP). The web application has a user-friendly genome-browser interface to facilitate the selection of the best target DNA sequences for experimental design.
An easy-to-use web-based tool for designing sgRNAs for SpCas9 nucleases on a genome scale. Cas-Database can be applied to construct optimal sgRNA libraries that target thousands of coding sequences in 12 different organisms for genome-wide knockout screening experiments. Because Cas-Database contains all available targets in CDS regions as well as target-related information, including data about potential off-target sites, users can easily access the data through the interactive web interface or web API. The web interface was made using cutting-edge web development techniques such as AJAX, so the website is highly responsive to user input and the output results load quickly.
Could be very beneficial to select single sgRNA with high potency from a pool of identified sgRNAs. ge-CRISPR is a web server which is an integrated pipeline to predict sgRNAs with high on target and minimum off target activity. The performance of ge-CRISPR pipeline is better than earlier methods as it holds potential to predict both quantitative and qualitative efficiencies of sgRNAs for diverse organisms. It will be useful to scientific community engaged in CRISPR research and therapeutics development.
A web service to help users design guide RNAs (gRNAs) optimized for specificity. CT-Finder accommodates the original single-gRNA Cas9 system and two specificity-enhancing paired-gRNA systems: Cas9 D10A nickases (Cas9n) and dimeric RNA-guided FokI nucleases (RFNs). Optimal target candidates can be chosen based on the minimization of predicted off-target effects. Graphical visualization of on-target and off-target sites in the genome is provided for target validation. Major model organisms are covered by this web service. The service covers major model organisms, including human, mouse, and Arabidopsis, and can be easily extended to other species. With its capability to accommodate three CRISPR systems, emphasis on target specificity, flexibility in user inputs of multiple parameter settings, and seamless integration into a genome browser, CT-Finder will empower many researchers in the gRNA design and optimal target determination of CRISPR-based genome editing.
CCTop / CRISPR/Cas9 target online predictor
A tool to determine suitable CRISPR/Cas9 target sites in a given query sequence(s) and predict its potential off-target sites. CCTop identifies and ranks all candidate sgRNA target sites according to their off-target quality and displays full documentation. CCTop was experimentally validated for gene inactivation, non-homologous end-joining as well as homology directed repair. CCTop is an experimentally validated system for the rapid selection of high quality target sites for gene inactivation, non-homologous end-joining as well as homology directed repair.
Helps in the design of optimal "guide" RNAs (gRNAs) by providing several protospacer adjacent motif (PAM) choices, a run-time definition of the seed and of the allowed number of mismatches, and a flexible output interface that allows sorting of the results, optional viewing/hiding of columns, etc. A key element of Off-Spotter is that it does not have a rigid definition of the seed: instead, the user can declare both the seed's location and extent on-the-fly. We expect that this flexibility in combination with Off-Spotter's speed and richly annotated output will enable experimenters to interactively and quickly explore different scenarios and gRNA possibilities.
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.
Guide Picker
Allows side-by-side correlative analysis of scoring functions. The CRISPR Guide Picker mode is an addition to the DESKGEN Cloud Platform. It allows user to visualize data from four sgRNA design parameters at one time. The tool can be used to support various experimental applications that require genome editing, including CRISPR knockout, CRISPR knockin, CRISPRa and CRISPRi. Guide Picker has built to help biologists stand on the shoulders of leading CRISPR genome editing labs all over the world.
COSMID / CRISPR Off-target Sites with Mismatches, Insertions, and Deletions
Predicts and ranks potential off-target cleavage sites and provides valuable guidance for guide strand designs. COSMID scores the potential off-target sites based on the number and location of base mismatches, allowing ranking of the more likely off-target sites. COSMID is unique in that it provides exhaustive genomic searches for off-target sites due to mismatches, deletions, and insertions, as well as providing primers for experimental validation of predicted off-target sites.
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.
EuPaGDT / Eukaryotic Pathogen gRNA Design Tool
Implements an effective on-target search algorithm to identify gRNA targeting multi-gene families, which play important roles in host–pathogen interactions. EuPaGDT assists users in designing single-stranded oligonucleotides for homology directed repair. In batch processing mode, it is able to process genome-scale sequences, enabling preparation of gRNA libraries for large-scale screening projects. Finally, EuPaGDT can facilitate researchers of eukaryotic pathogens to arrive at proper gRNA design for CRISPR-Cas9 experiments and thus bring new understanding for these otherwise difficult to manipulate pathogens.
Allows users to create tiling single guide RNAs (sgRNAs) for Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 system. sgTiler is developed for generating sgRNAs for any input DNA sequence, including genes or regulatory regions as well as for identifying sgRNAs in genic regions. The software intends to determine the off-target potential (OTP) of each candidate sgRNA thanks to user-provided annotations of important genomic features and to optimize the number and distribution of sgRNAs for covering an entire region.
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