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detect CRISPR sequences (version 0.1.5)

Input sequence as FASTA:

Minimum number of repeats a CRISPER must have:

Minimum length of a CRISPER repeated region:

Maximum length of a CRISPER repeated region:

Minimum length of CRISPER non repeated region:

or spacer region

Maximum length of CRISPER non repeated region:

or spacer region

Length of search window to used to discover CRISPERs:

Additional output format:

Please select a output format.

What it does

MinCED - Mining CRISPRs in Environmental Datasets

MinCED is a program to find 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. MinCED runs from the command-line and was derived from CRT (http://www.room220.com/crt/).

https://github.com/ctSkennerton/minced

Citation

For the underlying tool, please cite Bland C, Ramsey TL, Sabree F, Lowe M, Brown K, Kyrpides NC, Hugenholtz P: CRISPR Recognition Tool (CRT): a tool for automatic detection of clustered regularly interspaced palindromic repeats. BMC Bioinformatics. 2007 Jun 18;8(1):209

If you use this tool in Galaxy, please cite Gruening, BA et al. https://github.com/bgruening/galaxytools