BLAST (EBI)

BLAST (EBI) performs sequence similarity searches and local alignments of nucleotide and protein query sequences against reference sequence databases to identify homologs, support functional annotation, and enable evolutionary analyses.

Key Features:

• BLAST core algorithm: Implements the Basic Local Alignment Search Tool (BLAST) for local sequence alignments of nucleotide and protein sequences.
• Performance optimization: Reduces CPU time and memory usage by breaking long queries into manageable chunks and retrieving only relevant parts of lengthy subject sequences.
• Modular software library: Provides programmatic access to subject sequence data from multiple sources via a modular library.
• Strategy files: Supports saving and reusing sets of BLAST options through strategy files that can be uploaded to or downloaded from the NCBI BLAST website.
• Integration with EMBL-EBI resources: Operates within the EMBL-EBI Job Dispatcher framework and interoperates with resources including UniProt, InterPro, ENA, and Ensembl Genomes.
• Scalability and data handling: Updated to accommodate increasing data volumes for high-demand sequence analysis workloads.

Scientific Applications:

• Genomics: Identifying homologous genes and mapping sequence similarity across genomes for annotation and comparative genomics.
• Proteomics: Detecting homologous proteins and conserved domains to support protein function inference and annotation (linked to UniProt and InterPro data).
• Evolutionary biology: Reconstructing evolutionary relationships and identifying conserved and divergent sequence regions.
• Functional annotation: Transferring functional annotations to query sequences based on detected similarity to annotated database entries.

Methodology:

Computational steps include breaking long queries into manageable chunks, retrieving only relevant portions of subject sequences to limit CPU and memory use, and accessing subject sequence data via a modular software library.