GeneWise (EBI)

GeneWise aligns protein sequences to genomic DNA to predict gene structures and detect homologous coding regions while accommodating introns and frameshifting errors.

Key Features:

• Integration of gene prediction and homology searches: Combines protein-to-genome alignment with gene prediction to identify coding regions based on homology.
• Protein-to-genome alignment: Aligns protein sequences directly to genomic DNA to map coding regions onto genomic context.
• Handling of introns: Accounts for introns within genomic DNA during alignment and gene model prediction.
• Frameshift management: Detects and models frameshifting errors to produce accurate alignments despite insertions or deletions that shift reading frames.
• Detection of pseudogenes and transposon-related sequences: Identifies pseudogenes and transposon-associated sequences that can confound gene prediction and annotation.

Scientific Applications:

• Gene prediction in genomic regions: Applied to a 2.9-Mb region from Drosophila melanogaster to provide reasonably accurate gene predictions.
• Annotation refinement: Revealed cases where incorrect gene predictions arose from transposons with valid protein-coding genes or from pseudogenes, aiding genome annotation curation.

Methodology:

Integrates homology search techniques with gene prediction algorithms to align protein sequences with genomic DNA while modeling introns and potential frameshift mutations.