i-ADHoRE

i-ADHoRe identifies highly degenerated homology relations within and between genomic sequences by integrating gene content and gene order into profiles that detect homologous segments.

Key Features:

• Profile-based detection: Integrates gene content and gene order into comprehensive profiles to identify highly degenerated homologous segments.
• Profile alignment optimization: Implements algorithmic optimizations to improve performance of the profile alignment routine.
• Multi-genome analysis: Processes annotations from multiple genomes or genome parts concurrently to report intra- and inter-genomic homology.
• Homology reporting: Reports regions of homology both within single genomes and across different genomes.
• Implementation: Provides C++ source code for the core program together with Perl scripts and a Perl API for post-processing.

Scientific Applications:

• Evolutionary biology: Detects and analyzes genome rearrangement and conservation patterns to investigate evolutionary processes.
• Comparative genomics: Identifies conserved and degenerated homologous regions across species and genomes.
• Phylogenetics: Supports phylogenetic analyses by providing conserved synteny and homology information.

Methodology:

Constructs detailed profiles encapsulating gene content and gene order and performs optimized profile alignment to detect subtle homologous relationships, with support for concurrent processing of multiple genome annotations.