LALIGN (EBI)

LALIGN (EBI) identifies internal duplications by calculating non-intersecting local sequence alignments to detect similar regions within biological sequences.

Key Features:

• Local sequence alignment: Performs local alignments to detect regions of similarity within larger sequences without requiring end-to-end alignment.
• Non-intersecting alignments: Reports alignments that do not overlap, enabling clear delineation of distinct duplicated regions.
• Internal duplication detection: Identifies internal duplications within nucleotide or protein sequences as distinct alignment segments.
• EMBL-EBI Job Dispatcher integration: Operates within the EMBL-EBI Job Dispatcher sequence analysis framework.
• Programmatic access: Accessible via RESTful and SOAP-based APIs for automated sequence analysis workflows.
• Data integration: Can be used in conjunction with EMBL-EBI resources such as UniProt, InterPro, ENA, and Ensembl Genomes for sequence data input and interpretation.

Scientific Applications:

• Evolutionary analysis: Detects duplicated regions relevant to studies of gene duplication and molecular evolution.
• Comparative genomics: Identifies internal sequence similarities useful for inter-species and intra-genome comparisons.
• Functional genomics and structural variation: Supports identification of duplicated segments that may affect gene function or genomic structure.

Methodology:

Calculates local sequence alignments constrained to be non-intersecting and executes within the EMBL-EBI Job Dispatcher framework with programmatic access via RESTful and SOAP-based APIs.