SyntTax

SyntTax performs synteny analysis integrated with prokaryotic taxonomy to predict and analyze gene order conservation across archaeal and bacterial genomes.

Key Features:

• Integration with Taxonomy: Links synteny data to a hierarchical prokaryotic taxonomy and leverages coverage of completely sequenced prokaryotes to contextualize gene order conservation.
• Absynte-based Synteny Analysis: Implements and extends the Absynte algorithm to produce robust syntenies and to connect completely sequenced microbial genomes via taxonomic relationships.
• Conserved Gene Cluster Resolution: Resolves conserved complex gene clusters and has confirmed functional relationships, including identification of components of the E. coli YgjD multiprotein complex involved in tRNA modification.
• Evolutionary Clustering and Fusion Analysis: Analyzes evolution of gene clustering and alternative gene fusions to propose candidate proteins potentially interacting with established complexes.

Scientific Applications:

• Orthology Assessment: Assesses orthology by examining conserved genomic neighborhoods across prokaryotic species.
• Functional Gene Prediction: Predicts functional relationships between genes based on conserved synteny patterns.
• Complex Gene Cluster Analysis: Analyzes and resolves complex gene clusters to infer evolutionary conservation and biological significance.

Methodology:

Based on the Absynte algorithm and integration of synteny analysis with hierarchical prokaryotic taxonomy to connect completely sequenced microbial genomes.