ARBitrator

ARBitrator retrieves and curates gene sequences from NCBI GenBank to produce high-confidence homologues for genomic, phylogenetic, and functional analyses.

Key Features:

• Automated retrieval: Automates searches of NCBI GenBank for specified genes to collect candidate sequences.
• Two-step strategy: Employs an initial broad collection of potential homologues followed by a best-hit refinement step to prioritize relevant sequences.
• Conserved-domain screening: Refines candidate sets by screening for conserved domains to ensure functional relevance across taxa.
• Low false-positive rate: Produces curated sequence sets with an observed false-positive rate of approximately 0.033%.
• Adaptability: Originally developed for the nifH gene but applicable to other target genes for analogous retrieval and curation tasks.

Scientific Applications:

• Phylogenetic characterization: Provides curated gene sequences to support phylogenetic analyses of uncultivated and cultivated microorganisms.
• Sequence-based assay development: Supplies validated gene targets for designing molecular assays to detect specific microorganisms.
• Functional genomics of nitrogen fixation: Enables efficient collection of nifH and related gene sequences for studies of N2 fixation and associated environmental functions.

Methodology:

Performs a two-step computational workflow consisting of a broad homologous sequence collection from GenBank using comprehensive search criteria followed by a best-hit refinement that screens candidates for conserved domains.