Dataset Information

Casboundary: automated definition of integral Cas cassettes.

ABSTRACT:

Motivation

CRISPR-Cas are important systems found in most archaeal and many bacterial genomes, providing adaptive immunity against mobile genetic elements in prokaryotes. The CRISPR-Cas systems are encoded by a set of consecutive cas genes, here termed cassette. The identification of cassette boundaries is key for finding cassettes in CRISPR research field. This is often carried out by using Hidden Markov Models and manual annotation. In this article, we propose the first method able to automatically define the cassette boundaries. In addition, we present a Cas-type predictive model used by the method to assign each gene located in the region defined by a cassette's boundaries a Cas label from a set of pre-defined Cas types. Furthermore, the proposed method can detect potentially new cas genes and decompose a cassette into its modules.

Results

We evaluate the predictive performance of our proposed method on data collected from the two most recent CRISPR classification studies. In our experiments, we obtain an average similarity of 0.86 between the predicted and expected cassettes. Besides, we achieve F-scores above 0.9 for the classification of cas genes of known types and 0.73 for the unknown ones. Finally, we conduct two additional study cases, where we investigate the occurrence of potentially new cas genes and the occurrence of module exchange between different genomes.

Availability and implementation

https://github.com/BackofenLab/Casboundary.

Supplementary information

Supplementary data are available at Bioinformatics online.

SUBMITTER: Padilha VA

PROVIDER: S-EPMC8208735 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

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Publications

Casboundary: automated definition of integral Cas cassettes.

Padilha Victor A VA Alkhnbashi Omer S OS Tran Van Dinh VD Shah Shiraz A SA Carvalho André C P L F ACPLF Backofen Rolf R

Bioinformatics (Oxford, England) 20210601 10

<h4>Motivation</h4>CRISPR-Cas are important systems found in most archaeal and many bacterial genomes, providing adaptive immunity against mobile genetic elements in prokaryotes. The CRISPR-Cas systems are encoded by a set of consecutive cas genes, here termed cassette. The identification of cassette boundaries is key for finding cassettes in CRISPR research field. This is often carried out by using Hidden Markov Models and manual annotation. In this article, we propose the first method able to ...[more]

PMID: 33226067

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Dataset Information

Casboundary: automated definition of integral Cas cassettes.

Motivation

Results

Availability and implementation

Supplementary information

Publications

Casboundary: automated definition of integral Cas cassettes.

Similar Datasets

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