The DOI matches its Crossref record; 38 of the 38 references it cites were found in a registry or an index.
BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains
Open accessAbstract
Bacteriophages are broadly classified into two distinct lifestyles: temperate and virulent. Temperate phages are capable of a latent phase of infection within a host cell (lysogenic cycle), whereas virulent phages directly replicate and lyse host cells upon infection (lytic cycle). Accurate lifestyle identification is critical for determining the role of individual phage species within ecosystems and their effect on host evolution. Here, we present BACPHLIP, a BACterioPHage LIfestyle Predictor. BACPHLIP detects the presence of a set of conserved protein domains within an input genome and uses this data to predict lifestyle via a Random Forest classifier that was trained on a dataset of 634 phage genomes. On an independent test set of 423 phages, BACPHLIP has an accuracy of 98% greatly exceeding that of the previously existing tools (79%). BACPHLIP is freely available on GitHub ( https://github.com/adamhockenberry/bacphlip ) and the code used to build and test the classifier is provided in a separate repository ( https://github.com/adamhockenberry/bacphlip-model-dev ) for users wishing to interrogate and re-train the underlying classification model.
Overview
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Integrity signals
Registry
Cites
Statistics
Verification
Claims the paper makes
The claims and statistics of this paper haven’t been checked yet.
Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.
Self-check
Percentages, sums and reported differences re-computed from the paper’s own numbers.
The self-check needs the paper’s full text.
Citations
Cites
Cd-hit: Accelerated for clustering the next-generation sequencing data
Fu, L., Niu, B., Zhu, Z., Wu, S., & Li, W. (2012) · Bioinformatics · doi:10.1093/bioinformatics/bts565 · Cited by 11,175
Accelerated Profile HMM Searches
Eddy, S. R. (2011) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1002195 · Cited by 6,975
High throughput ANI analysis of 90K prokaryotic genomes reveals clear species boundaries
Jain, C., Rodriguez-R, L. M., Phillippy, A. M., Konstantinidis, K. T., & Aluru, S. (2018) · Nature Communications · doi:10.1038/s41467-018-07641-9 · Cited by 5,748 · cited 1×
“To ascertain whether hidden phylo- 61 genetic structure in our dataset was inflating test set accuracies, we conservatively clustered 62 all labeled phages (training and testing sets) using fastANI (27) and assessed BACPHLIP 63 accuracy separately on test data for which there were (and were not) genomes in the train-…”
CDD/SPARCLE: the conserved domain database in 2020
Lu, S., Wang, J., Chitsaz, F., Derbyshire, M. K., Geer, R. C., Gonzales, N. R., Gwadz, M., Hurwitz, D. I., Marchler, G. H., Song, J. S., et al. (2020) · Nucleic Acids Research · doi:10.1093/nar/gkz991 · Cited by 3,028
CheckV assesses the quality and completeness of metagenome-assembled viral genomes
Nayfach, S., Camargo, A. P., Schulz, F., Eloe-Fadrosh, E., Roux, S., & Kyrpides, N. C. (2021) · Nature Biotechnology · doi:10.1038/s41587-020-00774-7 · Cited by 1,750
Dedrick, R. M., Guerrero-Bustamante, C. A., Garlena, R. A., Russell, D. A., Ford, K., Harris, K., Gilmour, K. C., Soothill, J., Jacobs-Sera, D., Schooley, R. T., et al. (2019) · Nature Medicine · doi:10.1038/s41591-019-0437-z · Cited by 1,410
Paez-Espino, D., Eloe-Fadrosh, E. A., Pavlopoulos, G. A., Thomas, A. D., Huntemann, M., Mikhailova, N., Rubin, E., Ivanova, N. N., & Kyrpides, N. C. (2016) · Nature · doi:10.1038/nature19094 · Cited by 1,170
Phage diversity, genomics and phylogeny
Dion, M. B., Oechslin, F., & Moineau, S. (2020) · Nature Reviews Microbiology · doi:10.1038/s41579-019-0311-5 · Cited by 960
Lysogeny in nature: mechanisms, impact and ecology of temperate phages
Howard-Varona, C., Hargreaves, K. R., Abedon, S. T., & Sullivan, M. B. (2017) · The ISME Journal · doi:10.1038/ismej.2017.16 · Cited by 894
Patterns and ecological drivers of ocean viral communities
Brum, J. R., Ignacio-Espinoza, J. C., Roux, S., Doulcier, G., Acinas, S. G., Alberti, A., Chaffron, S., Cruaud, C., de Vargas, C., Gasol, J. M., et al. (2015) · Science · doi:10.1126/science.1261498 · Cited by 785
Cited by
Metagenomic compendium of 189,680 DNA viruses from the human gut microbiome
Nayfach, S., Páez-Espino, D., Call, L., Low, S. J., Sberro, H., Ivanova, N. N., Proal, A. D., Fischbach, M. A., Bhatt, A. S., Hugenholtz, P., et al. (2021) · Nature Microbiology · doi:10.1038/s41564-021-00928-6 · Cited by 580
Federici, S., Kredo-Russo, S., Valdés-Mas, R., Kviatcovsky, D., Weinstock, E., Matiuhin, Y., Silberberg, Y., Atarashi, K., Furuichi, M., Oka, A., et al. (2022) · Cell · doi:10.1016/j.cell.2022.07.003 · Cited by 542
Roux, S., Camargo, A. P., Coutinho, F. H., Dabdoub, S. M., Dutilh, B. E., Nayfach, S., & Tritt, A. (2023) · PLOS Biology · doi:10.1371/journal.pbio.3002083 · Cited by 466
Peng, Y., Lu, Z., Pan, D., Shi, L.-D., Zhao, Z., Liu, Q., Zhang, C., Jia, K., Li, J., Hubert, C. R. J., et al. (2023) · The ISME Journal · doi:10.1038/s41396-023-01491-0 · Cited by 48
(2024) · doi:10.1128/spectrum.03838-23 · Cited by 4
Metadata
- Authors
- Hockenberry, A. J., & Wilke, C. O.
- Venue
- PeerJ
- Publisher
- PeerJ
- Published
- 2021-05-06
- Volume
- 9
- Pages
- e11396
- ISSN
- 2167-8359 (ISSN-L)
- OpenAlex
- W3158178572
- Cited by
- 334
- References
- 38
- FWCI
- 22.90
- Type
- journal article
- Language
- en
- Open access
- gold
About these checks
Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.
Statistics and arithmetic are recomputed, not judged.
Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.
What counts as a claim ›How we measure confidence ›How we check this ›
Are you an author, or do you see a problem with this page? Request a review
How to cite
Cite CoChat for the checks on this page, and the paper for its own findings.
- This page
- CoChat. (2026). Citation check: BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains. https://app.cochat.ai/papers/10.7717/peerj.11396
- The paper
- Hockenberry, A. J., & Wilke, C. O. (2021). BACPHLIP: predicting bacteriophage lifestyle from conserved protein domains. PeerJ. https://doi.org/10.7717/peerj.11396
Data sources
Bibliographic data: Semantic Scholar, OpenAlex, Crossref.
Contains information from the Semantic Scholar Academic Graph Datasets, made available under the ODC Attribution License (ODC-BY 1.0).
Semantic Scholar’s data is described in: Kinney, R., et al. (2023). The Semantic Scholar Open Data Platform. arXiv:2301.10140.
