needle (EBI)

needle (EBI) performs global pairwise alignment of two biological sequences using the Needleman-Wunsch algorithm to determine optimal end-to-end sequence similarity.

Key Features:

• Needleman-Wunsch algorithm: Implements the Needleman-Wunsch algorithm for global alignment of two sequences.
• Global end-to-end alignment: Aligns entire sequences to optimize alignment at both sequence termini.
• EMBL-EBI Job Dispatcher integration: Executes within the EMBL-EBI Job Dispatcher framework for job submission and execution.
• Data resource integration: Interfaces with UniProt, InterPro, ENA, and Ensembl Genomes for reference data access.
• Programmatic access: Supports submission and retrieval via RESTful and SOAP-based APIs.

Scientific Applications:

• Comparative genomics: Compares full-length genomic or gene sequences to assess global sequence similarity.
• Evolutionary studies: Assesses overall sequence conservation and divergence across homologous sequences.
• Genomics research: Supports analyses that require whole-sequence alignment for genome- or gene-level comparisons.
• Proteomics and sequence comparison: Enables global alignment of protein sequences for comparative and functional inference.

Methodology:

Implements the Needleman-Wunsch global alignment algorithm and operates within the EMBL-EBI Job Dispatcher framework, with programmatic access via RESTful and SOAP APIs and linkage to UniProt, InterPro, ENA, and Ensembl Genomes.