Splign

Splign computes spliced alignments between cDNA (including ESTs) and genomic sequences to produce precise mappings for genome annotation, alternative splicing analysis, and study of pseudogenes and gene duplications.

Key Features:

• High-Performance Preliminary Alignment: Performs a rapid preliminary alignment step to identify candidate alignment regions for downstream processing.
• Compartment Identification Algorithm: Implements a compartmentalization algorithm that detects adjacent duplicated regions and potential gene duplications to separate paralogous alignments and aid pseudogene analysis.
• Refined Sequence Alignment: Executes refined spliced alignments that recognize introns and splice signals and handle non-consensus splice sites, small exons, paralogs, sequencing errors, and polymorphic sites.

Scientific Applications:

• Eukaryotic Genome Annotation: Produces precise cDNA-to-genome alignments to support annotation of eukaryotic genomes, including alignment of large datasets such as the human expressed sequence tag (EST) set.
• Alternative Splicing Studies: Identifies intron-exon structures and splice signals to support analysis of alternative splicing events.
• Pseudogene Research: Applies compartment identification to investigate pseudogenes and gene duplication events.

Methodology:

Combines a high-performance preliminary alignment, a compartmentalization algorithm for identifying adjacent duplicated regions, and a refined spliced alignment that recognizes introns and splice signals.