SpacePHARER: sensitive identification of phages from CRISPR spacers in 
prokaryotic hosts

Zhang, R.; Mirdita, M.; Levy Karin, E.; Norroy, C.; Galiez, C.; Söding, J.

doi:10.1093/bioinformatics/btab222

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SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts

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Zhang, R.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Mirdita, M.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Levy Karin, E.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Norroy, C.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Galiez, C.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Söding, J.
Research Group of Quantitative and Computational Biology, MPI for Biophysical Chemistry, Max Planck Society;

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Citation

Zhang, R., Mirdita, M., Levy Karin, E., Norroy, C., Galiez, C., & Söding, J. (2021). SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts. Bioinformatics, 37(19), 3364-3366. doi:10.1093/bioinformatics/btab222.

Cite as: https://hdl.handle.net/21.11116/0000-0009-6895-A

Abstract

SpacePHARER (CRISPR Spacer Phage–Host Pair Finder) is a sensitive and fast tool for de novo prediction of phage–host relationships via identifying phage genomes that match CRISPR spacers in genomic or metagenomic data. SpacePHARER gains sensitivity by comparing spacers and phages at the protein level, optimizing its scores for matching very short sequences, and combining evidence from multiple matches, while controlling for false positives. We demonstrate SpacePHARER by searching a comprehensive spacer list against all complete phage genomes.