Optimal Generators for a Systematic Block Code Model of Prokaryotic Translation Initiation

Research output: Contribution to journalConference article

4 Scopus citations

Abstract

The decoding of received error control encoded bit streams is fairly straightforward when the channel encoding algorithms are efficient and known. But if the encoding scheme is unknown or part of the data is missing, how would one design a viable decoder for the received transmission? Communication engineers may not frequently encounter this situation, but for computational biologists this is an immediate challenge as we attempt to decipher and understand the vast amount of sequence data produced by genome sequencing projects. Assuming the systematic parity check block code model of protein translation initiation, this work presents an approach for determining the generator matrix given a set of potential codewords. The resulting generators and corresponding parity matrices are applied to valid and invalid Escherichia coli K-12 MG1655 messenger RNA leader sequences. The generators constructed using strict subsets of the 16S ribosomal RNA performed better than those constructed using the (5,2) block code model in earlier work.

Original languageEnglish (US)
Pages (from-to)3858-3860
Number of pages3
JournalAnnual International Conference of the IEEE Engineering in Medicine and Biology - Proceedings
Volume4
StatePublished - 2003
EventA New Beginning for Human Health: Proceedings of the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society - Cancun, Mexico
Duration: Sep 17 2003Sep 21 2003

Keywords

  • Coding Theory
  • Prokaryotic Translation Initiation
  • Systematic Block Codes

ASJC Scopus subject areas

  • Signal Processing
  • Biomedical Engineering
  • Computer Vision and Pattern Recognition
  • Health Informatics

Fingerprint Dive into the research topics of 'Optimal Generators for a Systematic Block Code Model of Prokaryotic Translation Initiation'. Together they form a unique fingerprint.

Cite this