ArticleNucleic acids research2012
PhiSpy: a novel algorithm for finding prophages in bacterial genomes that combines similarity- and composition-based strategies.
Article in Nucleic acids research, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 366 papers.
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366 citing papers in PubMed, 559 citations in OpenAlex.
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- High-quality phage assembly from metagenomes with PALACE.Nature biotechnology · 2026Article
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- Lactiplantibacillus plantarum SLpl116 attenuates OVA-induced food allergy with ecological restoration of the gut microbiota and immune rebalancing.NPJ science of food · 2026Article
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- Whole-genome and Comparative Genomic Analysis Reveal the Biocontrol and Plant Growth-Promoting Potential of Bacillus velezensis JN.Y2 Against Oat Anthracnose.Functional & integrative genomics · 2026Article
- Helicobacter pylori phages: resource landscape, translational challenges, and engineered antibacterial strategies.Archives of microbiology · 2026Review
- Evidence for Genotype-Associated Differences in Disease Severity and Limitations of Serotype-Based Classification inPathogens (Basel, Switzerland) · 2026Article
- Whole-genome sequence of Rahnella aceris HPDA25 isolated from mycorrhizosphere of Gastrodia elata.BMC genomic data · 2026Article
306 more citing papers are in PubMed but not listed here.
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Authors and funding
3 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Prophages are phages in lysogeny that are integrated into, and replicated as part of, the host bacterial genome. These mobile elements can have tremendous impact on their bacterial hosts' genomes and phenotypes, which may lead to strain emergence and diversification, increased virulence or antibiotic resistance. However, finding prophages in microbial genomes remains a problem with no definitive solution. The majority of existing tools rely on detecting genomic regions enriched in protein-coding genes with known phage homologs, which hinders the de novo discovery of phage regions. In this study, a weighted phage detection algorithm, PhiSpy was developed based on seven distinctive characteristics of prophages, i.e. protein length, transcription strand directionality, customized AT and GC skew, the abundance of unique phage words, phage insertion points and the similarity of phage proteins. The first five characteristics are capable of identifying prophages without any sequence similarity with known phage genes. PhiSpy locates prophages by ranking genomic regions enriched in distinctive phage traits, which leads to the successful prediction of 94% of prophages in 50 complete bacterial genomes with a 6% false-negative rate and a 0.66% false-positive rate.
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