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CONSORF: a consensus prediction system for prokaryotic coding sequences.

Sungsoo Kang1, Sung-Jin Yang, Sangsoo Kim

  • 1KOBIC (Korean BioInformation Center), KRIBB, Daejeon 305-806 and Soongsil University, 1-1 Sangdo-dong, Dongjak-gu, Seoul 156-743, Korea.

Bioinformatics (Oxford, England)
|November 6, 2007
PubMed
Summary
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CONSORF is an automated system for identifying prokaryotic coding sequences (CDSs) using genome comparisons and ab initio predictions. It offers reliable CDS information, including frame-shifts and alternative start sites, accessible via a website.

Area of Science:

  • Bioinformatics
  • Genomics
  • Computational Biology

Background:

  • Accurate identification of prokaryotic coding sequences (CDSs) is crucial for genomic analysis.
  • Existing methods may require manual intervention or lack comprehensive information.

Purpose of the Study:

  • To introduce CONSORF, a fully automatic system for high-accuracy prokaryotic CDS identification.
  • To provide reliable CDS information, including prediction scores and alternative start sites.

Main Methods:

  • CONSORF predicts CDSs using consensus alignments from multiple genome-to-proteome comparisons (FASTX program).
  • It complements alignment-based predictions with consensus ab initio predictions for unannotated genomic regions.
  • The system integrates these predictions to generate comprehensive CDS information.

Related Experiment Videos

Main Results:

  • CONSORF delivers high-accuracy prokaryotic CDS identification.
  • The system provides prediction reliability scores, identifies predicted frame-shifts, and lists alternative start sites.
  • It also offers best pair-wise match information against other prokaryotes.

Conclusions:

  • CONSORF offers a robust and automated solution for prokaryotic CDS identification.
  • The system's comprehensive output facilitates downstream genomic research and analysis.
  • Web accessibility enhances the usability of CONSORF for the scientific community.