digIS

digIS detects distant and putative novel insertion sequence (IS) elements in prokaryotic genomes to enable discovery of mobile genetic elements involved in genome organization and evolution.

Key Features:

• Detection Capability: Detects both known IS elements and distant or putative novel IS elements beyond those identifiable by sequence similarity to existing IS family databases.
• Profile HMMs from Transposases: Employs profile hidden Markov models (HMMs) constructed from the catalytic domains of transposases to identify divergent IS elements.
• Benchmarking Performance: Demonstrates improved detection of distant and putative novel IS elements in comparative analyses with datasets that have manually curated annotations while maintaining moderate false positive rates.
• Input Formats and Annotation: Accepts contig sequences in FASTA format and can use an optional GenBank annotation file to assist classification of identified IS elements.
• Taxonomic Scope: Applicable to archaeal and bacterial genomes for large-scale genomic and metagenomic studies.

Scientific Applications:

• Genome Evolution Studies: Facilitates discovery of novel IS elements to study evolutionary dynamics and functional roles of mobile genetic elements within host genomes.
• Metagenomic Analysis: Enables detection of distant IS elements in metagenomic datasets where novel sequences are prevalent and traditional similarity-based methods are limited.

Methodology:

Uses profile hidden Markov models (HMMs) constructed from the catalytic domains of transposases; comparative analyses with datasets having manually curated annotations were used to evaluate detection performance and false positive rates.