webFlaGs

webFlaGs predicts protein functional associations by analyzing conservation of flanking genes in genomic neighborhoods to infer co-function and evolutionary relationships.

Key Features:

• Input and Processing: Accepts lists of NCBI protein accessions and uses sensitive sequence searching to cluster proteins based on neighborhood-encoded characteristics into homologous groups.
• Graphical Visualization: Produces graphical representations of gene neighborhoods that illustrate conservation patterns across different evolutionary levels.
• Phylogenetic Analysis: Generates phylogenetic trees annotated with flanking gene conservation data to trace lineage-specific evolution of gene clusters and operons.
• BLASTP Integration: Supports optional BLASTP searches against a reduced RefSeq database to generate input accession lists and analyze neighborhood conservation.

Scientific Applications:

• Molecular evolutionary analysis: Enables analysis of lineage-specific evolution of gene clusters and operons using conserved neighborhood patterns and annotated phylogenies.
• Discovery of novel functional associations: Facilitates identification of previously unrecognized functional associations, including discovery of toxin-antitoxin systems in prokaryotes and bacteriophages.

Methodology:

Sensitive sequence searching clusters proteins into homologous groups based on conservation of flanking genes; conserved gene neighborhoods are analyzed and visualized and used to annotate phylogenetic trees to predict protein functional associations, with optional BLASTP searches against a reduced RefSeq database to generate input accession lists.