SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts.
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ABSTRACT: Summary
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.Availability and implementation
SpacePHARER is available as an open-source (GPLv3), user-friendly command-line software for Linux and macOS: https://github.com/soedinglab/spacepharer.Supplementary information
Supplementary data are available at Bioinformatics online.
SUBMITTER: Zhang R
PROVIDER: S-EPMC8504623 | biostudies-literature | 2021 Oct
REPOSITORIES: biostudies-literature
Publications
SpacePHARER: sensitive identification of phages from CRISPR spacers in prokaryotic hosts.
Zhang Ruoshi R Mirdita Milot M Levy Karin Eli E Norroy Clovis C Galiez Clovis C Söding Johannes J
Bioinformatics (Oxford, England) 20211001 19
<h4>Summary</h4>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 ...[more]
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