ISfinder: the reference centre for bacterial insertion sequences

By Patricia Siguier, Jocelyne Pérochon, Laurent Lestrade, J. Mahillon, Michael Chandler. Nucleic Acids Res., 2005

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ISfinder () 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 It has superseded the Stanford reference center.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.

Subfields: Ecology, Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/61b6fb82656f3da3052ec003a8df4700e5fae715

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Citations in the corpus

Bacterial insertion sequences: their genomic impact and diversity (2014, methodology): “This role has been assumed by the ISfinder database (www-is.biotoul.fr) (Siguier et al., 2006) following the closure of the Stanford repository (Lederberg, 1981).”
Metagenomic analysis reveals wastewater treatment plants as hotspots of antibiotic resistance genes and mobile genetic elements. (2017, methodology): “In addition, local 171 databases of insertion sequences and integron integrase genes were created by downloading ISs 172 sequences from the ISfinder (Siguier et al., 2006) and integrase genes from the INTEGRALL (Moura 173 et al., 2009), respectively.”
Comparative Genomics of Plant-Associated Pseudomonas spp.: Insights into Diversity and Inheritance of Traits Involved in Multitrophic Interactions (2012, background): “fr/) [149]; only expectation values of 10(25) and below were considered as significant matches during searches.”
mobileOG-db: a Manually Curated Database of Protein Families Mediating the Life Cycle of Bacterial Mobile Genetic Elements (2021, background): “0 (11), COMPASS (21), NCBI Plasmid RefSeq (22), GutPhage Database (18), pVOG (17), ISfinder (19), ACLAME (23), and immedb (20).”
Insights from 20 years of bacterial genome sequencing (2015, background): “These newer technologies hold the promise of not only generating more sequence for less money, but they may eventually eliminate the concept of draft microbial genomes all together.”
MOB-suite: software tools for clustering, reconstruction and typing of plasmids from draft assemblies (2018, neutral): “The classified insertion sequence (IS) elements were parsed from the GenBank flat file and single queries were made to the ISFinder database [27] to classify IS elements not assigned to an IS family.”
Unicycler: Resolving bacterial genome assemblies from short and long sequencing reads (2016, background): “However, much Illumina sequencing uses short fragments (500 bp or less) that are smaller than many repetitive elements in bacterial genomes[1].”
ISsaga is an ensemble of web-based methods for high throughput identification and semi-automatic annotation of insertion sequences in prokaryotic genomes (2011, methodology): “This is integrated as a module into ISfinder, the prokaryote IS reference centre database [7] and IS repository, which includes more than 3,500 expertly annotated individual ISs from bacteria and archaea and also provides a basis for IS classification.”