geneHummus

geneHummus identifies and characterizes plant gene families by extracting RefSeq proteins and analyzing conserved domain architectures with SPARCLE to support comparative genomics and evolutionary analyses.

Key Features:

• Automated Annotation: Automates identification of gene family members through an R-based pipeline.
• RefSeq Protein Extraction: Extracts proteins from the RefSeq database with high specificity and sensitivity for gene family retrieval.
• Conserved Domain Architecture Identification: Uses SPARCLE (SPecies-Agnostic Retrieval of Conserved Domains by Local Exhaustive search) to identify conserved domain architectures within proteins.
• R-Based Framework: Implemented in R.

Scientific Applications:

• Comparative Genomics: Enables analysis of gene family expansion and evolution across species.
• Functional Inference: Supports inference of gene function via conserved domain architectures and family membership.
• Orphan Crop Genomics: Applicable to non-model plant systems, including characterization of gene families in Cicer arietinum (chickpea) and other legumes.
• Plant Breeding and Trait Discovery: Facilitates identification of candidate gene families relevant to development, adaptation, and breeding studies.

Methodology:

The pipeline extracts protein data from the RefSeq database, identifies conserved domain architectures using SPARCLE, and was applied in a case study on the auxin receptor factors (ARF) gene family in Cicer arietinum and other legumes.