ExoLocator

ExoLocator facilitates comparative analysis of protein-coding exons across vertebrate species by aggregating ENSEMBL-derived genomic and homology annotations and producing exon-level orthologous and paralogous alignments to study exon conservation and divergence.

Key Features:

• Data Aggregation: Aggregates genomic sequences together with exon and homology annotations from the ENSEMBL database of completed vertebrate genomes.
• Orthologous and Paralogous Alignments: Organizes exons into alignments that include both orthologous and paralogous sequences.
• Exon Search via Smith-Waterman: Employs a hardware-accelerated version of the Smith-Waterman algorithm to identify ostensibly missing exons in orthologous protein pairs across species.
• Computational Pipeline: Uses a computational pipeline to narrow search regions for candidate exons and to identify suitable templates from other species.
• Pairwise Alignment Algorithms: Incorporates state-of-the-art implementations of pairwise alignment algorithms for exon identification and comparison.
• Multiple Sequence Alignments: Produces nucleotide- and peptide-level multiple sequence alignments with annotated exon boundaries.

Scientific Applications:

• Evolutionary Biology: Supports analyses of gene evolution by comparing exon conservation and divergence among vertebrate species.
• Comparative Genomics: Enables comparative genomics studies by organizing exon-level orthologous and paralogous alignments across ENSEMBL genomes.
• Conservation and Functional Divergence Assessment: Facilitates estimation of conservation within orthologous sets and assessment of functional divergence across paralogues.

Methodology:

Aggregates ENSEMBL genomic sequences and exon/homology annotations; organizes exons into orthologous and paralogous alignments; applies a hardware-accelerated Smith-Waterman algorithm and state-of-the-art pairwise alignment implementations; uses a computational pipeline to narrow search regions and select templates; generates nucleotide and peptide multiple sequence alignments with exon boundary annotation.