Optimal generators for a systematic block code model of prokaryotic translation initiation.
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 block code model in earlier works.
- Research Organization:
- Sandia National Laboratories (SNL), Albuquerque, NM, and Livermore, CA (United States)
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- AC04-94AL85000
- OSTI ID:
- 1004360
- Report Number(s):
- SAND2003-3128C; TRN: US1100666
- Resource Relation:
- Conference: Proposed for presentation at the 25th Annual International Conference of the IEEE Engineering in Medicine and Biology Society held September 17-21, 2003 in Cancun, Mexico.
- Country of Publication:
- United States
- Language:
- English
Similar Records
Towards a biological coding theory discipline.
Detection and reconstruction of error control codes for engineered and biological regulatory systems.