Off-Spotter source code

Use the Off-Spotter web tool | Learn how to use Off-Spotter

If you use any of the below please cite: Pliatsika, V, and Rigoutsos, I (2015) Off-Spotter: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs Biol. Direct 10(1):4

 
In this page you can find the source code of Off-Spotter1. Off-Spotter is our new tool which identifies all genome hits of one or multiple gRNAs given in input and returns them to the user together with position, structure and annotation information. Off-Spotter is extremely fast and accurate.

Off-Spotter is also very flexible. You can use your own genome data and any number of annotation files. Also it is set up to work for 4 PAM sequences, NGG, NAG, NNNNACA and NNGRRT (where R is A or G). Upon completion it returns the chromosome number, strand, starting position, ending position, the input gRNA, the hit, the PAM, the number of mismatches, and annotation information.

Web Tool

WebTool_Off-SpotterOff-Spotter is also available as a web tool2. The web tool additionally provides numerous sorting and viewing options as well as statistic information for the hits. Click here to use our web tool.

 

 

Tutorial and version information

For more details on how to use the Off-Spotter web tool and source code please visit the Off-Spotter help page.

Terms and Conditions

This code (© 2015 Thomas Jefferson University, All Rights Reserved) was created by Venetia Pliatsika and Isidore Rigoutsos and is an implementation of the Off-Spotter algorithm that appears in Pliatsika, V, and Rigoutsos, I (2015) “Off-Spotter: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs” Biol. Direct 10(1):4.

Use of these codes is bound by the following terms and conditions:

Terms of Use:

This code can be freely used for research, academic and other non-profit activities.
Only one instance of the code may be used at a time, and then for only one concurrent user. You may not
use the code to conduct any type of application service, service bureau or time-sharing operation or to
provide any remote processing, network processing, network telecommunications or similar services to
any person, entity or organization, whether on a fee basis or otherwise. The code can be copied and
compiled on any platform for the use authorized by these terms and conditions. All copies of the code
must be accompanied by this note. The code cannot be modified without the written permission of the
Computational Medicine Center of Thomas Jefferson University https://cm.jefferson.edu

Commercial use is strictly prohibited. If you wish to use these codes commercially please contact the
Computational Medicine Center of Thomas Jefferson University: https://cm.jefferson.edu/contact-us/

THE CODE IS PROVIDED “AS IS” WITH NO REPRESENTATIONS OR WARRANTIES OF ANY KIND, EITHER EXPRESSED
OR IMPLIED. TO THE FULLEST EXTENT PERMISSIBLE PURSUANT TO APPLICABLE LAW. THOMAS JEFFERSON
UNIVERSITY, AND ITS AFFILIATES, DISCLAIM ALL WARRANTIES, EXPRESS OR IMPLIED, INCLUDING, BUT NOT
LIMITED TO, THE IMPLIED WARRANTIES OF TITLE, MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
NON-INFRINGEMENT.

NEITHER THOMAS JEFFERSON UNIVERSITY NOR ITS AFFILIATES MAKE ANY REPRESENTATION AS TO THE RESULTS
TO BE OBTAINED FROM USE OF THE CODE.

Downloads

Source code

Current version: 0.2.2, released 10/26/2015

You can download the Off-Spotter source files as a single compressed file by clicking below. See the changelog here.

498 Downloads

Unsupported older version:
362 Downloads

 

Remote submission tool

Current Version: 1.1, released 10/26/2015

You can also download this utility that enables you to submit data to Off-Spotter from your computer. Use this for automated queries, larger inputs, or several sequences.

Please be mindful of the other users and submit a few different queries at the same time.
308 Downloads

References

  1. Pliatsika, V, and Rigoutsos, I (2015) Off-Spotter: very fast and exhaustive enumeration of genomic lookalikes for designing CRISPR/Cas guide RNAs Biol. Direct 10(1):4
  2. Off-Spotter web tool

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