WebScipio

WebScipio reconstructs exon-intron gene structures from protein sequences and genome assemblies to annotate gene models and alternative splicing in eukaryotes.

Key Features:

• Gene Structure Prediction: Reconstructs exon-intron structures from protein queries and identifies intron-exon borders and splice sites.
• Handling Sequencing Errors: Accounts for sequencing errors and fragmented genome assemblies when mapping protein queries to genomic sequences.
• Cross-Species Gene Annotation: Performs cross-species searches for gene annotation enabling reconstruction of gene structures across divergent eukaryotic species.
• Mutually Exclusive Exons and Tandem Gene Duplicates: Detects clusters of mutually exclusive internal exons and identifies tandem gene duplicates using similarity of the encoded protein regions as a criterion.
• Short Exon and Splice Site Reconstruction: Reconstructs very short exons and intron splice sites and applies Needleman-Wunsch alignment for query segments not matched by BLAT.
• Integration with EST and cDNA Data: Maps expressed sequence tag (EST) and cDNA sequences onto reconstructed gene structures to facilitate detection of alternative splice variants.
• Extensive Genome Database: Accesses a database of over 3,400 genome assembly files from more than 1,100 sequenced eukaryotic species.

Scientific Applications:

• Gene Structure Analysis: Determines exon-intron organization and splice sites for individual genes.
• Protein Family Evolution: Supports analyses of protein family evolution by providing exon-intron mappings across species.
• Comparative Genomics: Enables comparative genomics studies by reconstructing homologous gene structures across divergent species.
• Alternative Splicing Research: Facilitates investigation of alternative splicing mechanisms including exon skipping, intron retention, and mutually exclusive splicing.

Methodology:

Processes significant hits from BLAT output, applies Needleman-Wunsch alignment to unmatched query segments, maps EST and cDNA data onto reconstructed gene structures, identifies intron-exon borders and splice sites, and searches for mutually exclusive exons based on similarity of the encoded protein regions while accounting for sequencing errors and fragmented assemblies.