SHOOT

SHOOT integrates query sequences into pre-existing phylogenetic trees to determine evolutionary relationships and identify orthologs across gene families.

Key Features:

• Phylogenetic Tree Integration: Integrates a user query sequence into an appropriate pre-existing phylogenetic tree drawn from a curated database of gene families.
• Ortholog Identification: Identifies orthologs across species based on the phylogenetic placement of the query sequence.
• Gene Family Mapping: Maps query sequences to gene families by their position within phylogenetic trees.
• Evolutionary History Analysis: Enables tracing of evolutionary events such as gene duplication, horizontal gene transfer, and lineage-specific adaptations via tree placement.
• Performance: Performs searches with speed comparable to BLAST and placement accuracy comparable to conventional tree inference methods.

Scientific Applications:

• Comparative Genomic Studies: Supports identification of orthologs and gene family relationships for comparative analyses across species.
• Functional Annotation: Assists prediction of gene function by comparing query sequences to characterized sequences within a phylogenetic context.
• Evolutionary Research: Facilitates study of evolutionary patterns and processes, including gene duplication, horizontal gene transfer, and lineage-specific adaptation.

Methodology:

Searches a user-provided query sequence against a curated database of phylogenetic trees and employs algorithms to place the query sequence within those trees, achieving rapid placement comparable to BLAST and accuracy comparable to conventional tree inference methods.