“WeREVIEW: CRISPR Tools” is a live on-line repository of computational tools to assist researches at different stages of a CRISPR/Cas experiment. In our web site, you can find an updated comprehensive list of tools, and search for those fulfilling your specific needs. You can also propose modifications to the data associated to the tools or the incorporation of new ones.
Computational tools are crucial in the process of designing a CRISPR/Cas experiment for the targeted modification of the genome of a generic organism. Due to the popularity of this methodology and the rapid pace at which it evolves and changes, new computational tools show up constantly. For the same reasons, together with the intrinsic high death-rate of bioinformatics tools, many of these tools become unavailable at some point. Consequently, the traditional ways to inform the community about the landscape of available tools (e.g. reviews in the scientific literature, which provide a “frozen” view of the field at a given time point) are not adequate for this fast-moving field.
“WeREVIEW: CRISPR Tools” is available at https://bioinfogp.cnb.csic.es/tools/wereview/crisprtools.
You can find additional information in the following reference. Please cite it when using the tool:
Rafael Torres-Perez, Juan A. Garcia-Martin, Lluis Montoliu, Juan C.
Oliveros* & Florencio Pazos*. (2019).
WeReview: CRISPR Tools-Live Repository of Computational Tools for Assisting CRISPR/Cas Experiments.
Bioengineering (Basel). 2019 Jul 25;6(3) Link
Contact: Juan Carlos Oliveros (email@example.com), Florencio Pazos (firstname.lastname@example.org).
The main interface of “WeREVIEW: CRISPR Tools” shows a table with the list of tools currently incorporated, together with their main features. The user can sort the list by any of these features, as well as search for those with particular characteristics. It is also possible to add comments, change the contents of the table and incorporate records for new tools.
To sort the table by any of the fields just press the up/down arrows in the corresponding column. To filter the list of tools by specific criteria press in the column headers (names of the features) and a search box shows up. Depending on the feature, this is either a free-text box or a set of checkboxes. The headers of the columns where filters are being applied are highlighted. Additionally, the filters currently being applied appear as blue blackground boxes above the table. To remove a filter, press the “x” contained on the upper-right corner of the corresponding blue box.
It is possible to combine many of these searches (filters) to perform complex queries (see example below).
The features currently incorporated (columns in the table, from left to right) are:
“Name”. Name of the tool. By clicking on it, you can access the web site of the tool.
“Available?”. Indicates whether the tool was available the last time checked. The most recent date the tool was checked for availability is also shown.
“Purpose”. Main goal of the tool: ‘oligo designer’, ‘database’ (database of pre-designed sets of oligos), ‘post-analysis’ (computational analysis of genomic data associated to a CRISPR/Cas experiment) or ‘other’.
“Platform”. The way the user can access the tool: ‘web’ (web interface), ‘command-line’ (local command-line text-based tool), ‘desktop’ (local desktop application with user graphical interface), ‘webapp’ (web application that can be accessed programmatically through an API) or ‘other’.
“Off-targets”. Indicates whether the tool is able to locate/score potential off-targets for the gRNA.
“Score oligos”. Indicates whether the tool is able to predict the binding efficiency of the gRNA to the intended target(s) in the genome.
“Search by”. How the intended genomic target has to be specified as input for the tool: ‘DNA sequence’, ‘gene ID’ or ‘genomic coordinates’.
“Enzyme”. List Cas nucleases that are compatible with the tool.
“PAM”. List of “protospacer adjacent motifs” the tool allows to be incorporated in the gRNA being designed. They can be specified using the standard IUPAC 1-letter codes for nucleotides (e.g. ‘N’ for any, ‘R’ for A or G, …).
“Organisms”. Organisms whose genomes are incorporated into the tool, so that they can be scanned for possible off-targets, etc. Common and scientific names are both included.
“Citations”. Number of articles citing the tool in PubMed Central. A plot representing the yearly citation profile is also shown, so that temporal trends related to the popularity of the tool can be assessed.
“Reference”. Bibliographic reference(s) of the tool. Its record(s) in PubMed can be accessed by clicking the PMID link.
“Comments”. Free-text area to store generic data that do not fit in any of the other fields.
Any user can suggest changes to the contents or the addition of a new tool. This is done under a wiki-like schema, without requiring any registration or credentials. Nevertheless, all suggested modifications/additions are moderated, and they have to be accepted by the authors before being incorporated.
For adding a new tool, press the “Add New CRISPR Tool” button in the top right corner and fill the form with the tool data. Some of the fields are free-text while in others you have to choose among a set of possible values. For the reference, just enter the PMID and the system will retrieve the corresponding record.
To change/edit the data for a given tool, just double-click in the corresponding table row.
In both cases, you can optionally enter an email address to get feedback from the developers, such as a confirmation if the proposed change is finally incorporated.
Imagine you are interested in designing a CRISPR/Cas experiment to knock-out a gene in mouse using the S. pyogenes Cas9 nuclease and whose gRNA requires ‘NGG’ as PAM in 3’. The tool should be accessible through a web interface. You also want to predict the affinity of the gRNA for the target sites.
To look for the tools fulfilling these criteria you apply the following filters by pressing the corresponding column headers: “Web” in ‘Platform’, the green check in “Score oligos”, type ‘NGG’ in “PAM” and ‘mouse’ in “Organisms”. With these restrictions, you obtain a list of tools suitable for your experiment. This list could be further inspected or filtered to select tools that are currently available, apparently widely used (i.e. highly cited), etc.
BioinfoGP CNB-CSIC 2019