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CRISPR detection software tools | Genome annotation

Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly…
CRISPRmap
Web

CRISPRmap

Provides a quick and detailed insight into repeat conservation and diversity of…

Provides a quick and detailed insight into repeat conservation and diversity of both bacterial and archaeal systems. CRISPRmap comprises the largest dataset of CRISPRs to date and enables…

CRISPRFinder
Web

CRISPRFinder

An interface to extract with precision and to further analyse clustered…

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…

CRISPRcompar
Web

CRISPRcompar

Proposes a set of bioinformatic tools assisting biologists in the development…

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…

CRISPRone
Web

CRISPRone

Provides annotation of CRISPR—Cas systems including (i) CRISPR arrays of…

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…

CRISPRDetect
Web
Desktop

CRISPRDetect

A web-based and command line tool, that enables accurate identification of…

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…

CRT
Desktop

CRT CRISPR Recognition Tool

Identifies CRISPRs in large DNA strings, such as genomes and metagenomes. CRT…

Identifies CRISPRs in large DNA strings, such as genomes and metagenomes. CRT was shown to be a significant improvement over the current technique for CRISPR identification using Patscan. CRT's…

CRISPI
Web

CRISPI

A dedicated environment on CRISPR in prokaryotic genomes that offers for the…

A dedicated environment on CRISPR in prokaryotic genomes that offers for the first time an up-to-date view of existing CRISPR (71 archaea totalling 291 CRISPR, and 987 bacteria totalling 2103 CRISPR)…

PILER-CR
Desktop

PILER-CR

A program specifically designed for the identification and analysis of CRISPR…

A program specifically designed for the identification and analysis of CRISPR repeats. Once a repeat has been identified by PILER-CR, more sensitive search tools such as BLAST can be used to find…

CRISPRDirection
Desktop

CRISPRDirection

Predicts the strand of the resulting crRNAs. The method uses as input CRISPR…

Predicts the strand of the resulting crRNAs. The method uses as input CRISPR repeat predictions. CRISPRDirection uses parameters that are calculated from the CRISPR repeat predictions and flanking…

CRISPRTarget
Web

CRISPRTarget

Predicts the most likely targets of CRISPR RNAs. This can be used to discover…

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…

Green Listed
Web

Green Listed

Designs custom Clustered Regularly Interspaced Short Palindromic Repeats…

Designs custom Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) screens targeting sets of genes defined by the user. Green Listed is a web-based tool facilitating the rapid design…

CRISPRleader
Desktop

CRISPRleader

An efficient approach to determining CRISPR leader boundaries by focusing on…

An efficient approach to determining CRISPR leader boundaries by focusing on leader sequence conservation within groupings based on the similarity of the repeats in the adjacent CRISPR arrays.…

CRF
Web

CRF CRISPR finder by Random Forest

Represents a tool for CRISPR (clustered regularly interspaced short palindromic…

Represents a tool for CRISPR (clustered regularly interspaced short palindromic repeats) detection in archaea and bacterial genomes that utilizes machine learning. CRF identifies the real CRISPR…

CRISPRtools
Web

CRISPRtools

Provides a generalized and simplified approach to generate null alleles in…

Provides a generalized and simplified approach to generate null alleles in mouse using CRISPR/ Cas9 by designing deletions that remove internal coding regions or critical exons. CRISPRtools is a…

CRISPRdigger
Desktop

CRISPRdigger

Provides a de novo clustered regularly interspaced short palindromic repeats…

Provides a de novo clustered regularly interspaced short palindromic repeats (CRISPRs) annotation program. CRISPRdigger focuses on detecting weak Direct Repeats (DRs) signals. It uses RepeatScout for…

PRAP
Desktop

PRAP Prokaryotic Repeats Annotation Program

Automates the analysis of repeats in both finished and draft genomes. It is…

Automates the analysis of repeats in both finished and draft genomes. It is aimed at identifying full spectrum repeats at the scale of the prokaryotic genome. Compared with the major existing repeat…

CRISPR-Analyser
Desktop

CRISPR-Analyser

Permits to create an index of every CRISPR site within the target genome.…

Permits to create an index of every CRISPR site within the target genome. CRISPR-Analyser is a module and a collection of C++ scripts that has the primary function of finding off targets for a CRISPR…

MinCED
Desktop

MinCED Mining CRISPRs in Environmental Datasets

Finds clustered regularly interspaced short palindromic repeats (CRISPRs) in…

Finds clustered regularly interspaced short palindromic repeats (CRISPRs) in full genomes or environmental datasets such as metagenomes, in which sequence size can be anywhere from 100 to 800 bp.

CRISPRdb
Dataset

CRISPRdb

Utilizes the CRISPRFinder program to identify putative CRISPRs and additional…

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…

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