CRISPR identification software tools | Shotgun metagenomic sequencing data analysis
Clustered regularly interspaced short palindromic repeats (CRISPR) constitute a bacterial and archaeal adaptive immune system that protect against bacteriophage (phage). Analysis of CRISPR loci reveals the history of phage infections and provides a direct link between phage and their hosts.
Identifies and reconstructs CRISPR loci from raw metagenomic data without the need for assembly or prior knowledge of CRISPR in the data set. CRISPR in assembled data are often fragmented across many contigs/scaffolds and do not fully represent the population heterogeneity of CRISPR loci. Crass identified substantially more CRISPR in metagenomes previously analysed using assembly-based approaches. The increased sensitivity, specificity and speed of Crass will facilitate comprehensive analysis of CRISPRs in metagenomic data sets, increasing our understanding of phage-host interactions and co-evolution within microbial communities.
CRT is a tool for fast, de novo identification of CRISPRs in long DNA sequences. CRT works by first detecting repeats that are separated by a similar distance, and then checking for other CRISPR specific requirements (e.g., the spacers need to be non-repeating and similarly sized). We modified CRT to consider incomplete repeats at the ends of contigs from whole-metagenome assembly, and call the modified program metaCRT.
Encodes transcriptome-scale events into DNA and assessing the cumulative gene expression of populations of cells. Record-seq mainly serves to record specific and complex transcriptional information. This software can be leveraged to generate sentinel cells and can potentially capture dose-dependent and transient exposure. It also suits for elucidating dose-dependent features of complex cellular response and record transient paraquat stimulation.
Serves for similarity search-based prediction. CRISPRAlign is a program that allows users to identify clustered regularly interspaced short palindromic repeats (CRISPRs) in a target sequence (a genome or a contig) that has repeats similar to a given CRISPR (query CRISPR). It performs by detecting substrings in the target sequence (or its reverse complement) that are similar to the repeat sequence of a query CRISPR.
Finds clustered regularly interspaced short palindromic repeats and associated proteins (CRISPR) for metagenomic data without relying on generic assembly. It identifies and assembles sequences of CRISPRs that contain both known and novel repeats. The tool can detect direct repeat (DR) sequences when read length is short or DR-spacer unit is long.