The ORFanage: an ORFan database

Area of Science:

• Genomics
• Bioinformatics
• Evolutionary Biology

Background:

• Newly sequenced genomes reveal numerous species-specific protein-coding open reading frames (ORFs).
• Understanding the evolutionary significance and function of these poorly conserved ORFs, termed ORFans, is crucial.
• ORFans can be unique to a single genome (singleton/paralogous) or found in closely related species (orthologous).

Purpose of the Study:

• To develop a comprehensive database for studying and classifying ORFans.
• To facilitate the identification of singleton, paralogous, and orthologous ORFans across various genomic subsets.
• To provide a resource for selecting targets for further genomic and evolutionary investigations.

Main Methods:

• Construction of the ORFanage database, integrating predicted ORFs from fully sequenced microbial genomes.
• Implementation of search functionalities to identify different types of ORFans within user-defined genome collections.
• Database accessibility via a web portal for broad research community use.

Main Results:

• The ORFanage database has been successfully created, containing predicted ORFs from microbial genomes.
• The database allows for the classification and retrieval of singleton, paralogous, and orthologous ORFans.
• The system enables flexible searching across selected subsets of genomes.

Conclusions:

• The ORFanage database serves as a valuable tool for the systematic study of ORFans.
• It facilitates research into the evolution and functional roles of lineage-specific genes.
• The database aids in identifying novel targets for in-depth genomic and evolutionary research.