FlaGs

FlaGs analyzes and visualizes conservation of gene neighborhoods to investigate operon and gene cluster evolution and infer functional associations between genes.

Key Features:

• Input (NCBI accessions): Accepts lists of NCBI protein accessions as input for extraction of gene neighborhoods.
• Homologous grouping: Clusters neighborhood-encoded proteins into homologous groups using sensitive sequence searching.
• BLASTP against reduced RefSeq: Performs BLASTP searches against a reduced RefSeq database to identify homologs and expand accession sets.
• Graphical visualization: Produces graphical representations of gene neighborhood conservation across genomes.
• Phylogenetic annotation: Generates phylogenetic trees annotated with flanking gene conservation.

Scientific Applications:

• Operon and gene cluster evolution: Comparative analysis of gene neighborhood conservation across evolutionary levels to study operon and cluster evolution.
• Functional association inference: Prediction of functional linkages between genes based on conserved flanking gene arrangements.
• Discovery of novel genetic systems: Identification of novel systems such as toxin-antitoxin modules in prokaryotes and bacteriophages.

Methodology:

Accepts NCBI protein accession lists; optionally performs BLASTP searches against a reduced RefSeq database; applies sensitive sequence searching to cluster neighborhood-encoded proteins into homologous groups; generates graphical gene neighborhood maps and can produce phylogenetic trees annotated with flanking gene conservation.