**CRISPRer** is a tool for genome-wide selection and assessment of CRISPR/Cas protospacers. CRISPRer offers three distinct tasks.

First, CRISPRer may search for protospacers with unique seed sequences, i.e., with seed sequences which occur only once in a given input genome.

Second, it may search for seed sequences that are orthogonal to the input genome, i.e., which do not occur in the given input genome.

Third, it may assess a set of user-provided protospacers by collecting several statistics about genome-wide perfect and imperfect matches to their seed sequences.

In the first select box, the CRISPRer task is selected. For the first option, "Find protospacers with unique seeds", a filter can be defined, which limits the output of CRISPRer to genomic regions, e.g., the exons of a gene. If, for instance, you want to limit the output to the exons of gene *EMX1*, you need to set the form field "Chromosomal locations" to

::

 chr2:73144604-73145501
 chr2:73151438-73151622
 chr2:73160916-73162020

When searching for unique seeds, CRISPRer produces two output files, one file in tabular format and one file in GFF format. For the latter file, you may additionally choose the GFF version of the output file. By default, the output is in GFF3 format. If the checkbox "Use GFF2" is selected, the output format is changed to GFF2.


For the second option, "Find orthogonal seeds", CRISPRer does not require additional parameters.

For the third option, "Assess user-defined protospacers", you need to paste a list of protospacers (in FastA format) into the text box "Protospacers".

The remaining parameters are identical for all CRISPRer tasks.
In the form field "Input data", input sequences must be supplied as a FastA file uploaded by the "Upload File" task in section "Get Data" of Galaxy.

For convenience, we provide several genomes in a data library. These data sets are based on the data of UCSC, MSU, and TAIR.
To obtain data from the library, select "Data Libraries" from the menu item "Shared Data" on top of this page, select the library "Genomes", 
put a checkmark on your desired data, make shure that "Import to current history" is selected from the drop-down box beneath, and click the button "Go".
Using the menu item "Analyze data", you get back to the start page of CRISPRer.
Now you find this data set in your own history, and can select it at input of CRISPRer.

In the following two form fields, you need to specify the length of the protospacer and the length of the seed at the 3' end of the protospacer, where the seed needs to be shorter than the complete protospacer.

The protospacer adjacent motif (PAM) can be specified as a pattern using all IUPAC DNA symbols. The default is the PAM of the Cas9 endonuclease of *Streptococcus pyogenes*, ``NGG``.

Finally, you can select if the sequence matching the PAM is included into the output. For task "Find orthogonal seeds", the PAM pattern instead of the matching sequence is appended to the seed sequence, if this box is checked.

For all three tasks, CRISPRer produces an output file in tabular format. The columns of the output file are explained on the result page of each CRISPRer run.
For the task "Find protospacers with unique seeds", CRISPRer additionally produces an output file in GFF format, which can be loaded into your favourite genome browser, e.g., `UCSC genome browser`_.

You can also install this web-application within your local Galaxy server. Instructions can be found at the CRISPRer_ page of Jstacs. 
There you can also download a command line version of CRISPRer.

If you experience problems using TALENoffer, please contact_ us.

.. _UCSC genome browser: http://genome.ucsc.edu
.. _CRISPRer: http://jstacs.de/index.php/CRISPRer
.. _contact: mailto:grau@informatik.uni-halle.de