BAT: an integrated pipeline for gene tree construction, annotation, and functional inference

Area of Science:

• Bioinformatics
• Computational Biology
• Genomics

Background:

• Gene family analysis requires integrating sequence data with functional information like motifs and expression patterns within a phylogenetic framework.
• The increasing volume of genomic data necessitates localized, flexible bioinformatic tools for targeted gene family studies.

Purpose of the Study:

• To present BLAST-Align-Tree (BAT), an automated bioinformatic pipeline for constructing and annotating gene family phylogenies.
• To enable researchers to explore gene trees with custom annotations, including experimental datasets, amino acid motifs, and protein domains.

Main Methods:

• BAT integrates BLAST searches against local genome databases with gene tree construction.
• The pipeline supports multiple annotation modes, visualizing experimental data, custom motifs (regex), and HMM protein domains.
• It operates locally, independent of external databases, allowing integration of custom genomes and datasets.

Main Results:

• The BAT pipeline automates the process of gene family phylogeny construction and annotation.
• Visualizations effectively display diverse datasets, including custom motifs and protein domains, within the phylogenetic context.
• Case studies demonstrate BAT's utility in inferring functions of homologous and orthologous genes.

Conclusions:

• BAT provides a flexible, local solution for fine-scale phylogenomic analysis of gene families.
• The pipeline supports diverse eukaryotic model organisms and is adaptable for various research needs.
• BAT empowers researchers to conduct in-depth functional exploration of gene families using project-specific resources.