Palidis: fast discovery of novel insertion sequences.

Victoria R Carr, Solon P Pissis, Peter Mullany, Saeed Shoaie, David Gomez-Cabrero, David L Moyes

Research output: Contribution to journalArticlepeer-review


The diversity of microbial insertion sequences, crucial mobile genetic elements in generating diversity in microbial genomes, needs to be better represented in current microbial databases. Identification of these sequences in microbiome communities presents some significant problems that have led to their underrepresentation. Here, we present a bioinformatics pipeline called Palidis that recognizes insertion sequences in metagenomic sequence data rapidly by identifying inverted terminal repeat regions from mixed microbial community genomes. Applying Palidis to 264 human metagenomes identifies 879 unique insertion sequences, with 519 being novel and not previously characterized. Querying this catalogue against a large database of isolate genomes reveals evidence of horizontal gene transfer events across bacterial classes. We will continue to apply this tool more widely, building the Insertion Sequence Catalogue, a valuable resource for researchers wishing to query their microbial genomes for insertion sequences.
Original languageEnglish (US)
JournalMicrobial genomics
StatePublished - Mar 10 2023

Bibliographical note

KAUST Repository Item: Exported on 2023-03-15
Acknowledgements: The project was supported by the Centre for Host-Microbiome Interactions, King’s College London, funded by the Biotechnology and Biological Sciences Research Council (BBSRC) grant BB/M009513/1 awarded to D.L.M. S.S. was supported by Engineering and Physical Sciences Research Council (EPSRC), EP/S001301/1, Biotechnology Biological Sciences Research Council (BBSRC) BB/S016899/1 and Science for Life Laboratory (SciLifeLab). S.P.P. is supported in part by the PANGAIA and ALPACA projects that have received funding from the European Union's Horizon 2020 research and innovation programme under the Marie Sklodowska-Curie grant agreements No. 872539 and 956229, respectively.


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