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Computational Identification of -1 Frameshift Signals

  • Sanghoon Moon
  • Yanga Byun
  • Kyungsook Han
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 3036)

Abstract

Ribosomal frameshifts in the -1 direction are used frequently by RNA viruses to synthesize a single fusion protein from two or more overlapping open reading frames. The slippery heptamer sequence XXX YYY Z is the best recognized of the signals that promote -1 frameshifting. We have developed an algorithm that predicts plausible -1 frameshift signals in long DNA sequences. Our algorithm is implemented in a working program called FSFinder (Frameshift Signal Finder). We tested FSFinder on 72 genomic sequences from a number of organisms and found that FSFinder predicts -1 frameshift signals efficiently and with greater sensitivity and selectivity than existing approaches. Sensitivity is improved by considering all potentially relevant components of frameshift signals, and selectivity is increased by focusing on overlapping regions of open reading frames and by prioritizing candidate frameshift signals. FSFinder is useful for analyzing -1 frameshift signals as well as discovering unknown genes.

Keywords

Mouse Mammary Tumor Virus Computational Identification Rous Sarcoma Virus Nucleic Acid Research Ribosomal Frameshift 
These keywords were added by machine and not by the authors. This process is experimental and the keywords may be updated as the learning algorithm improves.

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Copyright information

© Springer-Verlag Berlin Heidelberg 2004

Authors and Affiliations

  • Sanghoon Moon
    • 1
  • Yanga Byun
    • 1
  • Kyungsook Han
    • 1
  1. 1.School of Computer Science and EngineeringInha UniversityInchonKorea

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