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ISfinder / Insertion Sequences finder

A dedicated database for bacterial insertion sequences (ISs). 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.

OASIS / Optimized Annotation System for Insertion Sequences

A computational tool for automated annotation of insertion sequences (ISs). OASIS takes advantage of widely available transposase annotations to identify candidate ISs and then uses a computationally efficient maximum likelihood method of multiple sequence alignment to identify the edges of each element. Thanks to its speed and flexibility, OASIS is capable not only of providing detailed IS information for a single genome but also of annotating thousands of genomes within hours, making it a valuable high-throughput tool for a global investigation of IS distribution across diverse taxa.

IScan

Identifies transposase sequences, inverted repeats and candidate target direct repeats of insertion sequences (ISs) in complete genomes. IScan is able to identify ISs with an arbitrary number of ORFs, including ISs with ORFs encoded on both strands. IS annotation in existing genomes may be highly heterogeneous, because different researchers may use different annotation methods. A tool like IScan thus allows the user to create consistent IS annotation with multiple user-specified parameters (repeat length, sequence similarity to a reference family member, etc.) across multiple genomes. This consistency and flexibility is essential for detailed analyses of IS evolution across multiple genomes.