OrfPredictor: predicting protein-coding regions in EST-derived sequences

Abstract

OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with a hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where the coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. OrfPredictor is available at https://fungalgenome.concordia.ca/tools/OrfPredictor.html.

Figure 1

Categories of information derived from the EST sequences. (A) A typical full-length cDNA sequence including one or more stop codons in the 5′-UTR, a start codon and a stop codon. The coding region may contain multiple ATG codons encoding methionine and the 3′-UTR may harbor additional stop codons. (B) A full-length cDNA without a stop codon in the 5′-UTR. (C) A sequence containing a 5′-UTR with a stop codon and a portion of the coding region. (D) A sequence containing a 5′-UTR with a stop codon. (E) A sequence containing a 5′-UTR without a 5′ stop codon, and a portion of the coding region. (F) A sequence containing a portion of 5′-UTR without a 5′ stop codon. (G) A sequence containing the internal portion of a coding region with or without internal ATG codons. (H) A sequence containing a portion of the coding region with an internal ATG codon, a 3′ stop codon and 3′-UTR. (I) A sequence containing a portion of the coding region with no internal ATG codons, a 3′ stop codon and a 3′-UTR. (J) A sequence containing a 3′-UTR without a 3′ stop codon. Red star: stop codon at 5′ end; green circle: start codon; blue circle: internal ATG codon; red hexagon: stop codon; solid line: sequenced portion of the full-length cDNA; and dashed line: unsequenced or truncated portion of the full-length cDNA.

Figure 2

The OrfPredictor server interface for loading data and choosing other parameters.