Seeker: alignment-free identification of bacteriophage genomes by deep learning Article Swipe
Noam Auslander
,
Ayal B. Gussow
,
Sean Benler
,
Yuri I. Wolf
,
Eugene V. Koonin
·
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkaa856
YOU?
·
· 2020
· Open Access
·
· DOI: https://doi.org/10.1093/nar/gkaa856
Recent advances in metagenomic sequencing have enabled discovery of diverse, distinct microbes and viruses. Bacteriophages, the most abundant biological entity on Earth, evolve rapidly, and therefore, detection of unknown bacteriophages in sequence datasets is a challenge. Most of the existing detection methods rely on sequence similarity to known bacteriophage sequences, impeding the identification and characterization of distinct, highly divergent bacteriophage families. Here we present Seeker, a deep-learning tool for alignment-free identification of phage sequences. Seeker allows rapid detection of phages in sequence datasets and differentiation of phage sequences from bacterial ones, even when those phages exhibit little sequence similarity to established phage families. We comprehensively validate Seeker's ability to identify previously unidentified phages, and employ this method to detect unknown phages, some of which are highly divergent from the known phage families. We provide a web portal (seeker.pythonanywhere.com) and a user-friendly Python package (github.com/gussow/seeker) allowing researchers to easily apply Seeker in metagenomic studies, for the detection of diverse unknown bacteriophages.
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Metadata
- Type
- article
- Language
- en
- Landing Page
- https://doi.org/10.1093/nar/gkaa856
- https://academic.oup.com/nar/article-pdf/48/21/e121/34658500/gkaa856.pdf
- OA Status
- gold
- Cited By
- 127
- References
- 53
- Related Works
- 10
- OpenAlex ID
- https://openalex.org/W3091956242
All OpenAlex metadata
Raw OpenAlex JSON
- OpenAlex ID
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https://openalex.org/W3091956242Canonical identifier for this work in OpenAlex
- DOI
-
https://doi.org/10.1093/nar/gkaa856Digital Object Identifier
- Title
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Seeker: alignment-free identification of bacteriophage genomes by deep learningWork title
- Type
-
articleOpenAlex work type
- Language
-
enPrimary language
- Publication year
-
2020Year of publication
- Publication date
-
2020-09-22Full publication date if available
- Authors
-
Noam Auslander, Ayal B. Gussow, Sean Benler, Yuri I. Wolf, Eugene V. KooninList of authors in order
- Landing page
-
https://doi.org/10.1093/nar/gkaa856Publisher landing page
- PDF URL
-
https://academic.oup.com/nar/article-pdf/48/21/e121/34658500/gkaa856.pdfDirect link to full text PDF
- Open access
-
YesWhether a free full text is available
- OA status
-
goldOpen access status per OpenAlex
- OA URL
-
https://academic.oup.com/nar/article-pdf/48/21/e121/34658500/gkaa856.pdfDirect OA link when available
- Concepts
-
Bacteriophage, Biology, Metagenomics, Computational biology, Identification (biology), Genome, Human virome, Python (programming language), Sequence (biology), DNA sequencing, Genetics, Sequence analysis, Gene, Computer science, Escherichia coli, Botany, Operating systemTop concepts (fields/topics) attached by OpenAlex
- Cited by
-
127Total citation count in OpenAlex
- Citations by year (recent)
-
2025: 17, 2024: 30, 2023: 35, 2022: 26, 2021: 16Per-year citation counts (last 5 years)
- References (count)
-
53Number of works referenced by this work
- Related works (count)
-
10Other works algorithmically related by OpenAlex
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