ssearch2seq (EBI)

ssearch2seq performs optimal local sequence alignments using the Smith-Waterman algorithm within the EMBL-EBI Job Dispatcher sequence analysis framework to compare protein and nucleic acid sequences.

Key Features:

• EMBL-EBI Job Dispatcher integration: Integrated into the EMBL-EBI Job Dispatcher sequence analysis framework for submission and execution of alignment jobs.
• Database integration: Accesses UniProt, InterPro, ENA, and Ensembl Genomes for reference sequence and annotation data during analyses.
• Smith-Waterman implementation: Implements the Smith-Waterman algorithm to generate optimal local alignments.
• Programmatic access: Supports RESTful and SOAP-based APIs for programmatic job submission and result retrieval.
• Sequence type support: Supports pairwise comparisons of protein and nucleic acid sequences.

Scientific Applications:

• Sequence alignment: Identifying regions of similarity between biological sequences that may indicate functional, structural, or evolutionary relationships.
• Protein and nucleic acid analysis: Enabling detailed pairwise analysis of protein and nucleic acid sequences to assess properties and interactions.

Methodology:

ssearch2seq employs the Smith-Waterman algorithm to find optimal local alignments between two sequences.