GeneSeqer

GeneSeqer predicts exon–intron gene structures in plant genomes by performing spliced alignments of expressed sequence tags (ESTs) and full-length cDNAs to genomic sequences within the PlantGDB database.

Key Features:

• Splice Site Prediction and Spliced Alignment: Performs spliced alignment using source-native ESTs, full-length cDNAs, and non-native probes derived from putative homologous genes to predict exon–intron boundaries and splice sites.
• Integration with PlantGDB: Organizes EST sequences into contigs representing tentative unique genes and links these contigs to genomic DNA within the PlantGDB repository.
• Gene Prediction and Cross-Species Comparisons: Integrates multiple bioinformatics tools to support gene prediction and to identify gene sets common across plants or specific to particular species.
• Community Annotation Support: Supports expert and community annotation by integrating public plant sequence evidence with predicted gene structures for curation.
• Functional Annotation and Gene Ontology Assignment: Annotates EST contigs by similarity to known protein sequences and assigns tentative Gene Ontology terms based on those similarities.
• Species-specific Transcript Evidence Presentation: Provides genome browsers for species such as Arabidopsis thaliana and Oryza sativa that present available EST and cDNA evidence for current transcript models.

Scientific Applications:

• Annotation Refinement: Refines existing gene annotations by improving exon–intron boundary and transcript model accuracy using EST and cDNA evidence.
• De novo Annotation of Draft Genomes: Enables de novo annotation of draft genomic sequences by aligning transcript evidence to genomic DNA.
• Comparative Genomics and Gene Family Analysis: Facilitates cross-species comparisons to identify conserved and species-specific gene sets.
• Expert and Community Curation: Supports community-driven expert annotation workflows by consolidating sequence evidence and predicted structures for curation.
• Functional Characterization: Aids functional annotation of putative translation products through similarity searches and tentative GO term assignment.

Methodology:

Uses spliced alignment of ESTs and full-length cDNAs to genomic sequences; employs non-native probes from putative homologous genes; organizes ESTs into contigs; performs similarity-based annotation to known protein sequences with tentative Gene Ontology assignment; and integrates multiple bioinformatics tools for gene prediction and cross-species comparison.