Gypsy Database (GyDB)

Gypsy Database (GyDB) classifies mobile genetic elements and related viruses by phylogeny to support evolutionary and sequence-based analysis of LTR retroelements and Caulimoviridae pararetroviruses.

Key Features:

• Phylogenetic classification: Organizes elements by lineage and protein-domain classifications with emphasis on LTR retroelements and related taxa (Ty3/Gypsy, Ty1/Copia, Bel/Pao, Retroviridae, Caulimoviridae).
• Protein-based phylogenies: Provides protein-based phylogenetic trees with distinct classifications assigned to various mobile elements.
• GyDB collection: Includes multiple sequence alignments, lineage-specific hidden Markov models (HMMs), and consensus sequences assembled as the GyDB collection.
• Analytical tools: Integrates BLAST and HMM servers for sequence characterization of new LTR retroelement and caulimovirus queries and links models to updated RefSeq databases.
• Curated content: Curates detailed descriptions and reviews for Ty3/Gypsy, Retroviridae, Ty1/Copia, Bel/Pao LTR retroelements, and Caulimoviridae pararetroviruses.

Scientific Applications:

• Evolutionary reconstruction: Reconstructs evolutionary relationships among LTR retroelements, pararetroviruses, and related mobile elements using protein phylogenies and HMMs.
• Sequence annotation and classification: Enables characterization and taxonomic assignment of novel LTR retroelements and caulimoviruses via BLAST and HMM-based model searches against curated datasets and RefSeq.
• Genome-evolution studies: Supports investigation of the roles of retroelements and pararetroviruses in genome evolution and function.

Methodology:

Protein-based phylogenetic classification using multiple sequence alignments, lineage-specific HMMs and consensus sequences, supplemented by BLAST and HMM searches integrated with RefSeq.