HSDFinder

HSDFinder identifies highly similar duplicate genes (HSDs) within eukaryotic nuclear genomes to annotate, categorize, and visualize gene duplications for studies of evolutionary and adaptive processes.

Key Features:

• Identification and annotation: Detects HSDs using BLAST-based sequence alignment and annotates duplicate gene sets.
• Categorization and visualization: Categorizes HSDs by sequence similarity and visualizes results via heatmaps and KEGG pathway mappings.
• Cross-species analysis: Supports comparative analysis of HSDs across eukaryotes including Chlamydomonas reinhardtii, Arabidopsis thaliana, Oryza sativa, Zea mays, and Chlamydomonas sp. UWO241.
• Integration with external tools: Integrates BLAST for alignments, InterProScan for protein domain analysis, and KEGG for pathway mapping.

Scientific Applications:

• Evolutionary mechanism analysis: Enables investigation of gene duplication as a mechanism shaping genome evolution.
• Adaptive versus nonadaptive evolution: Facilitates analysis of HSDs to distinguish adaptive and nonadaptive evolutionary patterns.
• Comparative genomics and adaptation: Supports studies of how gene duplications contribute to genomic diversity and species-specific adaptation.

Methodology:

HSDFinder uses BLAST-based sequence alignment to detect HSDs, performs annotation and categorization by similarity, applies InterProScan for protein domain analysis, and generates heatmap visualizations and KEGG pathway mappings.