The DOI matches its Crossref record; 29 of the 29 references it cites were found in a registry or an index.
Phamerator: a bioinformatic tool for comparative bacteriophage genomics
Open accessAbstract
BACKGROUND: Bacteriophage genomes have mosaic architectures and are replete with small open reading frames of unknown function, presenting challenges in their annotation, comparative analysis, and representation. RESULTS: We describe here a bioinformatic tool, Phamerator, that assorts protein-coding genes into phamilies of related sequences using pairwise comparisons to generate a database of gene relationships. This database is used to generate genome maps of multiple phages that incorporate nucleotide and amino acid sequence relationships, as well as genes containing conserved domains. Phamerator also generates phamily circle representations of gene phamilies, facilitating analysis of the different evolutionary histories of individual genes that migrate through phage populations by horizontal genetic exchange. CONCLUSIONS: Phamerator represents a useful tool for comparative genomic analysis and comparative representations of bacteriophage genomes.
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Self-citationOrigins of Highly Mosaic Mycobacteriophage Genomes
Pedulla, M. L., Ford, M. E., Houtz, J. M., Karthikeyan, T., Wadsworth, C., Lewis, J. A., Jacobs-Sera, D., Falbo, J., Gross, J., Pannunzio, N. R., et al. (2003) · Cell · doi:10.1016/s0092-8674(03)00233-2 · Cited by 652
Self-citationPfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins
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Self-citationThe origins and ongoing evolution of viruses
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Jordan, T. C., Burnett, S. H., Carson, S., Caruso, S. M., Clase, K., DeJong, R. J., Dennehy, J. J., Denver, D. R., Dunbar, D., Elgin, S. C. R., et al. (2014) · mBio · doi:10.1128/mbio.01051-13 · Cited by 509
Self-citationHatfull, G. F. (2018) · Microbiology Spectrum · doi:10.1128/microbiolspec.gpp3-0026-2018 · Cited by 112
Self-citationMycobacteriophages: From Petri dish to patient
Hatfull, G. F. (2022) · PLOS Pathogens · doi:10.1371/journal.ppat.1010602 · Cited by 74
Self-citationPodgorski, J. M., Freeman, K., Gosselin, S., Huet, A., Conway, J. F., Bird, M., Grecco, J., Patel, S., Jacobs-Sera, D., Hatfull, G., et al. (2023) · Structure · doi:10.1016/j.str.2022.12.012 · Cited by 32
Self-citationWottrich, S., Mendonca, S., Safarpour, C., Nguyen, C., Marinelli, L. J., Hancock, S. P., Modlin, R. L., & Parker, J. M. (2024) · Microbiome Research Reports · doi:10.20517/mrr.2023.42 · Cited by 7
Metadata
- Authors
- Cresawn, S. G., Bogel, M., Day, N., Jacobs-Sera, D., Hendrix, R. W., & Hatfull, G. F.
- Venue
- BMC Bioinformatics
- Published
- 2011-10-12
- Volume
- 12
- Issue
- 1
- Pages
- 395-395
- ISSN
- 1471-2105 (ISSN-L)
- OpenAlex
- W2091728028
- Cited by
- 462
- References
- 29
- FWCI
- 9.44
- Type
- journal article
- Language
- en
- Open access
- gold
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