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

Xiang Jia Min1, Gregory Butler, Reginald Storms

  • 1Centre for Structural and Functional Genomics, Concordia University, Montreal, Quebec, Canada H4B 1R6.

Nucleic Acids Research
|June 28, 2005
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Summary
This summary is machine-generated.

OrfPredictor identifies protein-coding regions in expressed sequence tag (EST) data. This tool aids in annotating EST sequences, especially for large-scale projects, by predicting coding regions and providing sequence data.

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Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Expressed sequence tags (ESTs) are valuable for gene discovery but often require accurate identification of protein-coding regions.
  • Efficient annotation of ESTs is crucial for large-scale genomic projects to understand gene function and structure.

Purpose of the Study:

  • To develop and present OrfPredictor, a web server for predicting protein-coding regions within EST-derived sequences.
  • To provide a tool that facilitates the annotation of EST sequences, particularly in the context of high-throughput sequencing projects.

Main Methods:

  • OrfPredictor utilizes BLASTX alignments to identify translation reading frames for coding region prediction.
  • For sequences without a BLASTX hit, it predicts the most probable coding region based on intrinsic sequence signals.
  • The server outputs predicted peptide sequences in FASTA format with detailed annotation, including query ID, reading frame, and nucleotide positions.

Main Results:

  • OrfPredictor successfully predicts protein-coding regions in EST sequences.
  • The tool provides essential annotation data, including reading frame and start/end nucleotide positions.
  • The output facilitates downstream analysis and gene annotation efforts.

Conclusions:

  • OrfPredictor is an effective web server for identifying protein-coding regions in ESTs.
  • The tool streamlines the annotation process for EST-derived sequences, supporting large-scale genomic research.
  • OrfPredictor is accessible online for researchers to utilize in their projects.