Pseudofinder

Pseudofinder identifies pseudogene candidates in annotated GenBank files from bacterial and archaeal genomes to detect gene inactivation and signatures of relaxed selection.

Key Features:

• Reference-based multi-pronged detection: Employs a reference-based, multi-pronged approach to identify a broad spectrum of pseudogenes.
• Detection of highly degraded pseudogenes: Identifies highly degraded pseudogenes that are often overlooked by conventional gene-calling pipelines.
• Detection of newly formed pseudogenes: Detects newly formed pseudogenes characterized by minimal inactivating mutations.
• Identification of relaxed-selection candidates: Detects intact genes under relaxed selection pressure that may represent early stages of pseudogenization.
• Input format: Operates on annotated GenBank files from bacterial and archaeal genomes.
• Designed for prokaryotic genomes: Targets gene-dense prokaryotic genomes where pseudogenes can be rare or subtle.

Scientific Applications:

• Functional potential assessment: Identification and analysis of pseudogenes to assess the functional potential encoded within sequenced microbial genomes.
• Evolutionary dynamics: Investigation of evolutionary dynamics that shape bacterial and archaeal genomes.
• Population and ecological effects: Exploration of how ecological shifts or extreme population bottlenecks influence genome composition, gene inactivation, and pseudogenization.

Methodology:

Analyzes annotated GenBank files using a multi-pronged, reference-based computational approach to identify degraded and newly formed pseudogenes and to detect intact genes under relaxed selection pressure.