BPM

BPM performs distributed sequence analysis and comparative genomics by coordinating BLAST alignments, phylogenetic profiling, and MCL clustering across the European Grid Infrastructure (EGI).

Key Features:

• Modular components: BLAST alignment, phylogenetic profiling, and MCL clustering are implemented as three core modules that can operate independently or in combination.
• Mode 1 — BLAST-based clustering: Clusters protein query and database sequences based on BLAST output criteria.
• Mode 2 — Phylogenetic profiling: Generates phylogenetic profiles for each query sequence using the genomes associated with the database proteins.
• Mode 3 — Profile-guided MCL clustering: Performs MCL clustering of protein queries guided by generated phylogenetic profiles.
• Mode 4 — Integrated clustering and profiling: Integrates outputs from Mode 1 and Mode 3.
• Mode 5 — All-vs-all/pangenome analysis: Supports all-vs-all sequence comparisons for pangenome analyses by using identical files for query and database inputs.
• Distributed execution on EGI: Automatically distributes processes and data across available computational resources on the European Grid Infrastructure to scale processing.
• Performance: Reports up to a 14x improvement in processing speed over traditional methods.
• Compatibility: Maintains compatibility with BLAST, MCL, and phylogenetic profiling workflows and accepts FASTA-formatted protein sequences.

Scientific Applications:

• Comparative genomics: Enables large-scale comparative genomics analyses through sequence alignment, clustering, and phylogenetic profiling.
• Enzyme pathway and functional group identification: Supports targeted investigations of enzyme pathways within custom databases to identify functional groups.
• Pangenome analyses: Facilitates pangenome analyses via all-vs-all sequence comparisons and clustering.
• Evolutionary and functional inference: Assists inference of functionality and evolutionary relationships through combined alignment, profiling, and clustering.

Methodology:

Performs BLAST alignments, generates phylogenetic profiles from database genomes, applies MCL clustering, accepts FASTA-formatted query and database protein sequences plus a text file listing genomes and a configuration file for mode selection, and distributes tasks across the European Grid Infrastructure (EGI).