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RVDB-prot, a reference viral protein database and its HMM profiles.
Thomas Bigot1, Sarah Temmam2, Philippe Pérot2
1Hub de Bioinformatique et Biostatistique - Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France.
F1000Research
|October 1, 2020
Summary
We introduce RVDB-prot, a protein database for virus research, enhancing sequence comparisons. It offers reliable, annotated entries and Hidden Markov Model (HMM) profiles for sensitive protein searching.
Area of Science:
- Virology
- Bioinformatics
- Genomics
Background:
- Nucleic acid sequence databases are crucial for virus identification and characterization.
- Protein sequence analysis offers complementary and sometimes more sensitive approaches for biological sequence comparisons.
- The need for specialized protein databases in virology is growing with advancements in sequencing technologies.
Purpose of the Study:
- To introduce RVDB-prot, a comprehensive protein sequence database for viruses.
- To provide a resource for sensitive protein sequence comparisons in virology.
- To complement existing nucleic acid databases with protein-level data and analysis tools.
Main Methods:
- Development of RVDB-prot as the protein equivalent of the Virus non-redundant Reference Database (RVDB).
- Inclusion of reliable and accurately annotated unique protein entries.
- Integration of a Hidden Markov Model (HMM) protein profiles database for enhanced searching capabilities.
Main Results:
- Creation of RVDB-prot, a dedicated protein database for viral sequences.
- Facilitation of more sensitive protein sequence comparisons compared to traditional methods.
- Provision of HMM profiles enabling distant protein homology searches.
Conclusions:
- RVDB-prot serves as a valuable resource for the scientific community, particularly in virology.
- The database enhances the ability to identify and analyze viral proteins.
- RVDB-prot, alongside its nucleic acid counterpart RVDB, offers a more complete toolkit for viral research.
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