RVDB-prot

RVDB-prot provides a curated protein reference database for viral sequences, supplying uniquely annotated protein entries and Hidden Markov Model (HMM) profiles to improve sensitivity and accuracy of protein sequence comparisons and distant protein searches in virology research.

Key Features:

• Hidden Markov Model (HMM) profiles: Includes HMM profiles for protein families to enable detection of remote homologs and distant protein searches.
• Uniquely annotated protein entries: Contains meticulously curated and uniquely annotated viral protein sequences as reference entries.
• Enhanced sensitivity for sequence comparison: Provides resources optimized to increase sensitivity and accuracy of protein sequence comparisons.
• Support for distant homology detection: Facilitates identification of homologous sequences not apparent through direct sequence comparison methods.

Scientific Applications:

• Phylogenetic studies: Enables phylogenetic analyses of viral proteins using curated protein references and HMM-based similarity detection.
• Functional annotation: Supports functional annotation of viral proteins through homology detection and profile-based searches.
• Evolutionary analyses: Facilitates exploration of viral evolution and diversity by detecting remote similarities among viral proteins.
• Investigation of virus-host interactions and pathogenicity: Aids identification of homologous proteins relevant to virus-host interactions, pathogenicity, and potential therapeutic targets.

Methodology:

Provision of uniquely annotated protein entries and construction/use of Hidden Markov Model (HMM) profiles for distant protein searches and protein sequence comparisons.