Decoding algorithms using side-effect machines

Bioinformatics applies computers to problems in molecular biology. Previous research has not addressed edit metric decoders. Decoders for quaternary edit metric codes are finding use in bioinformatics problems with applications to DNA. By using side effect machines we hope to be able to provide efficient decoding algorithms for this open problem. Two ideas for decoding algorithms are presented and examined. Both decoders use Side Effect Machines(SEMs) which are generalizations of finite state automata. Single Classifier Machines(SCMs) use a single side effect machine to classify all words within a code. Locking Side Effect Machines(LSEMs) use multiple side effect machines to create a tree structure of subclassification. The goal is to examine these techniques and provide new decoders for existing codes. Presented are ideas for best practices for the creation of these two types of new edit metric decoders.

Name thesis:degree_name

M.Sc. Computer Science

Level thesis:degree_level

Masters

Discipline thesis:degree_discipline

Faculty of Mathematics and Science

Department dc:contributor.department

Department of Computer Science

Grantor

Brock University

Year dc:date.issued

2010

Author dc:creator

• Brown, Joseph Alexander

• Computer algorithms.
• Bioinformatics

Language dc:language.iso

eng

Handle dc:identifier.uri

http://hdl.handle.net/10464/2941

OAI identifier oai:identifier

oai:brocku.scholaris.ca:10464/2941