CRISPR · Software
MinCED
Identifies CRISPR arrays in complete genomes and assembled metagenomic contigs.
What MinCED is
MinCED (Mining CRISPRs in Environmental Datasets) is a command-line software utility designed to detect Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in genomic and environmental sequence datasets. It was created by Florent Angly and Connor Skennerton.
The software addresses the need to identify CRISPR arrays within both assembled metagenomes and full organismal genomes. It was derived from the CRISPR Recognition Tool (CRT) to facilitate repeat finding across diverse sequencing datasets.
Identifying CRISPR loci enables researchers to analyse adaptive immune systems in prokaryotes, characterise repeat-spacer arrays, and annotate microbial and viral defence systems within environmental or isolate sequences.
How it works
MinCED operates on FASTA-formatted nucleotide sequences, searching input sequences for patterns characteristic of CRISPR loci. The implementation is derived from CRT (CRISPR Recognition Tool) and runs via a Java-based command-line interface.
The search behaviour can be adjusted for specific sequence types; for example, researchers can lower the minimum number of repeats required to identify CRISPR elements within shorter contigs or fragments. Results can be exported as standard text tables or as GFF annotation files.
Key facts
- Full name
- Mining CRISPRs in Environmental Datasets
- Derivation
- CRISPR Recognition Tool (CRT)
- Input format
- FASTA sequence files (.fa, .fna)
- Output formats
- Text table (.txt, .crisprs) and GFF (.gff)
- Language
- Java
What you can use it for
- Whole-genome CRISPR array discovery
- Scanning complete microbial genomes, such as Escherichia coli, to locate and annotate CRISPR repeat-spacer arrays.
- Metagenomic contig screening
- Identifying CRISPR loci across assembled metagenomic contigs derived from environmental sequencing projects.
- Short-sequence repeat detection
- Searching for arrays with reduced repeat thresholds in shorter sequences by lowering the minimum repeat parameter.
Run it here
The research agent sets MinCED up on its machine the first time a task needs it, then runs it and reads the output back to you. Nothing to install on your side.
Try asking
“Find CRISPR arrays in this genome with MinCED and list the spacers.”
Strengths and limits
Good at
- Directly analyses both complete isolate genomes and assembled metagenomic contigs.
- Generates both tabular summary files and standard GFF annotation files simultaneously.
- Provides adjustable repeat thresholds to facilitate detection across sequences of varying lengths.
Watch out for
- Requires an external Java runtime environment to execute.
- Not intended for identifying CRISPRs directly from raw short reads in the 100–200 bp range, for which dedicated tools like Crass are recommended.
Questions
Can I run MinCED online without installing it?
The research agent sets MinCED up on its machine the first time a task needs it, then runs it and reads the output back to you. Nothing to install on your side.
What licence is MinCED under?
GPL-3.0. The terms are published at https://github.com/ctSkennerton/minced.
Can MinCED process raw short reads directly from sequencing instruments?
No. For detecting CRISPRs in raw short reads spanning 100 to 200 base pairs, the developers advise using tools designed specifically for that purpose, such as Crass.
What system dependencies are required to run MinCED?
MinCED requires Java, along with the wrapper executable and the compiled JAR file located in the same directory.
What output file formats does MinCED support?
It can output results to plain text summary files or structured GFF files, and can write both formats simultaneously in a single run.
How to cite it
Charles Bland et al., CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats, BMC Bioinformatics 8, no. 1 (2007): 209.
Written from MinCED's own README and project page. Statements citing a figure that does not appear there are removed before publication. Licence and running details come from our registry.