G-Mo.R-Se

G-Mo.R-Se constructs de novo gene models directly from RNA-Seq short reads to infer gene structures and splicing in genomes lacking prior annotations.

Key Features:

• De novo gene modelling: Builds gene models from RNA-Seq short reads without relying on existing genomic annotations or known splicing events.
• Short-read and exon-exon junction handling: Aligns short RNA-Seq reads across potential exon-exon junctions to reconstruct exon structures despite read brevity.
• Application to complex genomes: Demonstrated on the grapevine genome, showing capability to model genes in eukaryotic genomes with complex splicing patterns.

Scientific Applications:

• Evolutionary biology: Enables analysis of gene structure evolution in species that lack comprehensive annotations.
• Comparative genomics: Provides de novo gene models to support genomic comparisons across unannotated or poorly annotated genomes.
• Functional genomics: Supplies gene structures for interpretation of transcriptomic data and gene function studies.
• Novel gene and alternative splicing discovery: Facilitates identification of previously unannotated genes and alternative splicing events from RNA-Seq data.

Methodology:

Processes RNA-Seq short reads, aligns reads across potential exon-exon junctions, and assembles inferred exon and gene structures into de novo gene models.