OrfPredictor

OrfPredictor predicts protein-coding regions (open reading frames) from expressed sequence tag (EST) and cDNA-derived nucleotide sequences to support accurate coding-sequence annotation.

Key Features:

• Identification of Coding Regions: Predicts ORFs and coding regions by analyzing EST- or cDNA-derived query sequences.
• BLASTX Integration: Uses translation reading frames from BLASTX alignments to infer coding regions for sequences with BLASTX hits.
• Intrinsic Signal Analysis: Analyzes intrinsic signals within nucleotide sequences to identify probable coding regions when no BLASTX hits are available.
• Output Format: Outputs predicted peptide sequences in FASTA format with definition lines listing query ID, translation reading frame, and nucleotide start and end positions.

Scientific Applications:

• Genomic annotation of EST datasets: Annotates coding regions in large-scale EST and cDNA projects to support sequence-based gene catalogs.
• Functional genomics and expression analysis: Provides predicted ORFs to aid interpretation of gene expression patterns and downstream functional analyses.

Methodology:

Employs two approaches: BLASTX-based prediction that leverages translation reading frames from BLASTX alignments, and intrinsic signal-based prediction that analyzes intrinsic signals when BLASTX yields no hit.