The DOI matches its Crossref record; 31 of the 31 references it cites were found in a registry or an index.
ISEScan: automated identification of insertion sequence elements in prokaryotic genomes
Open accessAbstract
Motivation: The insertion sequence (IS) elements are the smallest but most abundant autonomous transposable elements in prokaryotic genomes, which play a key role in prokaryotic genome organization and evolution. With the fast growing genomic data, it is becoming increasingly critical for biology researchers to be able to accurately and automatically annotate ISs in prokaryotic genome sequences. The available automatic IS annotation systems are either providing only incomplete IS annotation or relying on the availability of existing genome annotations. Here, we present a new IS elements annotation pipeline to address these issues. Results: ISEScan is a highly sensitive software pipeline based on profile hidden Markov models constructed from manually curated IS elements. ISEScan performs better than existing IS annotation systems when tested on prokaryotic genomes with curated annotations of IS elements. Applying it to 2784 prokaryotic genomes, we report the global distribution of IS families across taxonomic clades in Archaea and Bacteria. Availability and implementation: ISEScan is implemented in Python and released as an open source software at https://github.com/xiezhq/ISEScan. Supplementary information: Supplementary data are available at Bioinformatics online.
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Cited by
Kent, A. G., Vill, A. C., Shi, Q., Satlin, M. J., & Brito, I. L. (2020) · Nature Communications · doi:10.1038/s41467-020-18164-7 · Cited by 216
Gut microbiota drives structural variation of exogenous probiotics to enhance colonization
Jiang, S., Huang, S., Zhang, Z., Ma, W., Han, Z., Song, Y., Huo, D., Cui, W., & Zhang, J. (2025) · Gut Microbes · doi:10.1080/19490976.2025.2503371 · Cited by 15
Metadata
- Authors
- Xie, Z., & Tang, H.
- Venue
- Bioinformatics
- Publisher
- Oxford University Press (OUP)
- Published
- 2017-07-06
- Volume
- 33
- Issue
- 21
- Pages
- 3340-3347
- ISSN
- 1367-4803 (ISSN-L)
- 1367-4811
- OpenAlex
- W2726257503
- Cited by
- 489
- References
- 31
- FWCI
- 3.69
- Type
- journal article
- Language
- en
- Open access
- hybrid
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