BIOMAT Database Logo BIOMAT Database Logo

Palidis: fast discovery of novel insertion sequences. 2023

Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
Parasites and Microbes, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, UK.

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.

UI MeSH Term Description Entries
D004251 DNA Transposable Elements Discrete segments of DNA which can excise and reintegrate to another site in the genome. Most are inactive, i.e., have not been found to exist outside the integrated state. DNA transposable elements include bacterial IS (insertion sequence) elements, Tn elements, the maize controlling elements Ac and Ds, Drosophila P, gypsy, and pogo elements, the human Tigger elements and the Tc and mariner elements which are found throughout the animal kingdom. DNA Insertion Elements,DNA Transposons,IS Elements,Insertion Sequence Elements,Tn Elements,Transposable Elements,Elements, Insertion Sequence,Sequence Elements, Insertion,DNA Insertion Element,DNA Transposable Element,DNA Transposon,Element, DNA Insertion,Element, DNA Transposable,Element, IS,Element, Insertion Sequence,Element, Tn,Element, Transposable,Elements, DNA Insertion,Elements, DNA Transposable,Elements, IS,Elements, Tn,Elements, Transposable,IS Element,Insertion Element, DNA,Insertion Elements, DNA,Insertion Sequence Element,Sequence Element, Insertion,Tn Element,Transposable Element,Transposable Element, DNA,Transposable Elements, DNA,Transposon, DNA,Transposons, DNA
D006801 Humans Members of the species Homo sapiens. Homo sapiens,Man (Taxonomy),Human,Man, Modern,Modern Man
D001419 Bacteria One of the three domains of life (the others being Eukarya and ARCHAEA), also called Eubacteria. They are unicellular prokaryotic microorganisms which generally possess rigid cell walls, multiply by cell division, and exhibit three principal forms: round or coccal, rodlike or bacillary, and spiral or spirochetal. Bacteria can be classified by their response to OXYGEN: aerobic, anaerobic, or facultatively anaerobic; by the mode by which they obtain their energy: chemotrophy (via chemical reaction) or PHOTOTROPHY (via light reaction); for chemotrophs by their source of chemical energy: CHEMOLITHOTROPHY (from inorganic compounds) or chemoorganotrophy (from organic compounds); and by their source for CARBON; NITROGEN; etc.; HETEROTROPHY (from organic sources) or AUTOTROPHY (from CARBON DIOXIDE). They can also be classified by whether or not they stain (based on the structure of their CELL WALLS) with CRYSTAL VIOLET dye: gram-negative or gram-positive. Eubacteria
D056186 Metagenomics The systematic study of the GENOMES of assemblages of organisms. Community Genomics,Environmental Genomics,Population Genomics,Genomics, Community,Genomics, Environmental,Genomics, Population
D019295 Computational Biology A field of biology concerned with the development of techniques for the collection and manipulation of biological data, and the use of such data to make biological discoveries or predictions. This field encompasses all computational methods and theories for solving biological problems including manipulation of models and datasets. Bioinformatics,Molecular Biology, Computational,Bio-Informatics,Biology, Computational,Computational Molecular Biology,Bio Informatics,Bio-Informatic,Bioinformatic,Biologies, Computational Molecular,Biology, Computational Molecular,Computational Molecular Biologies,Molecular Biologies, Computational
D064349 Genome, Microbial The genetic complement of a microorganism as represented in its DNA or in some microorganisms its RNA. Genomes, Microbial,Microbial Genome,Microbial Genomes

Related Publications

Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
Fast and accurate discovery of degenerate linear motifs in protein sequences.
January 2014, PloS one,
Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
Discovery of Novel Sequences in 1,000 Swedish Genomes.
January 2020, Molecular biology and evolution,
Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
Insertion sequences.
September 1998, Microbiology and molecular biology reviews : MMBR,
Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
Bacterial insertion sequences.
January 1996, Current topics in microbiology and immunology,
Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
Fast discovery and visualization of conserved regions in DNA sequences using quasi-alignment.
January 2013, BMC bioinformatics,
Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
ISCce1 and ISCce2, two novel insertion sequences in Clostridium cellulolyticum.
February 2003, Journal of bacteriology,
Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
RecMotif: a novel fast algorithm for weak motif discovery.
December 2010, BMC bioinformatics,
Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
Phenotypic screening-the fast track to novel antibody discovery.
March 2017, Drug discovery today. Technologies,
Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
Assembly-free discovery of human novel sequences using long reads.
December 2022, DNA research : an international journal for rapid publication of reports on genes and genomes,
Victoria R Carr, and Solon P Pissis, and Peter Mullany, and Saeed Shoaie, and David Gomez-Cabrero, and David L Moyes
FAST: FAST Analysis of Sequences Toolbox.
January 2015, Frontiers in genetics,
Copied contents to your clipboard!