ISfinder: the reference centre for bacterial insertion sequences
Open accessAbstract
ISfinder (www-is.biotoul.fr) is a dedicated database for bacterial insertion sequences (ISs). It has superseded the Stanford reference center. One of its functions is to assign IS names and to provide a focal point for a coherent nomenclature. It is also the repository for ISs. Each new IS is indexed together with information such as its DNA sequence and open reading frames or potential coding sequences, the sequence of the ends of the element and target sites, its origin and distribution together with a bibliography where available. Another objective is to continuously monitor ISs to provide updated comprehensive groupings or families and to provide some insight into their phylogenies. The site also contains extensive background information on ISs and transposons in general. Online tools are gradually being added. At present an online Blast facility against the entire bank is available. But additional features will include alignment capability, PsiBLAST and HMM profiles. ISfinder also includes a section on bacterial genomes and is involved in annotating the IS content of these genomes. Finally, this database is currently recommended by several microbiology journals for registration of new IS elements before their publication.
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The natural ISSpn6 TnpA can also mobilize using additional left and right ends within the locus.
“additionally revealing that the ISSpn6 TnpA can also mobilize using additional left and right ends within the locus”
From Sequence modeling and design from molecular to genome scale with Evo (2024) · cites this paper as [71]
The Introduction (page unavailable) explains that insertion-sequence DNA ends are important for mobility, but does not discuss ISSpn6 or TnpA. Searches for ISSpn6 TnpA and for mobilization using alternative ends found no passage addressing the claimed use of additional left and right ends within the locus. (LLM, conf=0.76)
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Cites
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IS231–MIC231 elements from Bacillus cereus sensu lato are modular
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Mobile Genetic Elements Associated with Antimicrobial Resistance
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“coli our databank contained all IS present in IS Finder [67].”
BackgroundTransposon-associated TnpB is a programmable RNA-guided DNA endonuclease
Karvelis, T., Druteika, G., Bigelyte, G., Budre, K., Zedaveinyte, R., Silanskas, A., Kazlauskas, D., Venclovas, Č., & Siksnys, V. (2021) · Nature · doi:10.1038/s41586-021-04058-1 · Cited by 348 · see citing works
Bridge RNAs direct programmable recombination of target and donor DNA
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“Sequences with alignments to known transposases were annotated based on tID as follows; >50% tID: annotated as “transposase,” 35–50% tID: annotated as “similar to transposase,” 10–35% tID: annotated as “possible transposase,” ORFs in all of those categories, as well as those annotated as transposases by the RAST autom…”
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“Insertion sequences were predicted by using IS finder.(20) Assessment of global genomic co-linearity relationships among species was performed by using the mauve software.”
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Selleri, E., Tarracchini, C., Petraro, S., Mancabelli, L., Milani, C., Turroni, F., Shao, Y., Browne, H. P., Lawley, T. D., van Sinderen, D., et al. (2026) · mSystems · doi:10.1128/msystems.01173-25 · Cited by 3 · see citing works
- Authors
- Siguier, P.
- Affiliations
- Centre National de la Recherche Scientifique (FR)
- Corresponding author
- Siguier, P.
- ORCID
- Siguier, P.
- Venue
- Nucleic Acids Research
- Publisher
- Oxford University Press (OUP)
- Published
- 2006-01-01
- Volume
- 34
- Issue
- 90001
- Pages
- D32-D36
- ISSN
- 0305-1048 (ISSN-L)
- 1362-4962
- PMC
- PMC1347377
- OpenAlex
- W2149452073
- Cited by
- 2,767
- References
- 8
- Citations by year
- 2026: 230 · 2025: 269 · 2024: 297 · 2023: 286 · 2022: 300 · 2021: 263 · 2020: 204 · 2019: 151 · 2018: 137 · 2017: 116 · 2016: 99 · 2015: 74 · 2014: 68 · 2013: 61 · 2012: 48
- FWCI
- 7.76
- Type
- journal article
- Language
- en
- Open access
- gold
- doi.org
- Licence
- public-domain
- Locations
- Nucleic Acids Research (publishedVersion, public-domain)
- Europe PMC (PubMed Central) (publishedVersion)
- PubMed Central (publishedVersion)
- PubMed (publishedVersion)
- HAL (submittedVersion)
- Digital Access to Libraries (Université catholique de Louvain (UCL), l'Université de Namur (UNamur) and the Université Saint-Louis (USL-B)) (submittedVersion, other-oa)
- Funders
- Centre National de la Recherche Scientifique
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Phylogenetic Studies
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Medicine › Antibiotic Resistance in Bacteria
- Keywords
- insertion sequences, bacterial transposons
- MeSH terms
- DNA Transposable Elements, DNA, Bacterial, User-Computer Interface, Genome, Bacterial, Internet, Databases, Nucleic Acid
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