INDELSCAN

INDELSCAN identifies and classifies genome-wide insertion and deletion (indel) events to distinguish species-specific indels and support functional and comparative genomic analyses.

Key Features:

• Multiple-sequence alignment strategy: Employs multiple sequence alignments incorporating one target species, one subject species, and one or more out-group species to improve discrimination of species-specific indels.
• Indel classification: Identifies and classifies four indel types — target species-specific, subject species-specific, non-species-specific, and pair-wise indels between the target and subject species — by referencing out-group sequences to distinguish insertions from deletions.
• Genomic location mapping: Maps indels to genomic features including 5' untranslated regions (5' UTR), introns, coding sequences (CDS), 3' untranslated regions (3' UTR), and intergenic regions.
• Taxonomic coverage: Includes nine predefined target species—Homo sapiens, Mus musculus, Rattus norvegicus, Canis familiaris, Monodelphis domestica, Gallus gallus, Danio rerio, Drosophila melanogaster, and Saccharomyces cerevisiae—and over 35 subject/out-group species spanning yeasts to mammals.
• Support for custom data: Supports indel identification from user-uploaded alignments and annotations.

Scientific Applications:

• Evolutionary biology: Enables identification of species-specific indels to study genome evolution and infer lineage-specific changes.
• Functional genomics: Facilitates analysis of indel impacts on gene structure and function by mapping events to 5' UTR, introns, CDS, 3' UTR, and intergenic regions.
• Comparative genomics: Supports comparative analyses across multiple taxa to detect conserved and divergent genomic regions and to distinguish insertions from deletions.

Methodology:

Uses multiple-sequence alignments of one target, one subject, and one or more out-group species; references out-group sequences to infer insertion versus deletion events and classify indel types; maps indels to genomic annotations and accepts user-provided alignments and annotations.