Title :
Edit metric decoding: Representation strikes back
Author :
Hughes, John ; Brown, J.A. ; Houghten, Sheridan ; Ashlock, Daniel
Author_Institution :
Comput. Sci., Brock Univ., St. Catharines, ON, Canada
Abstract :
Quaternary error-correcting codes defined over the edit metric may be used as labels to track the origin of sequence data. When used in such applications there are typically additional restrictions that are biologically motivated, such as a required GC content or the avoidance of certain patterns. As a result such codes can not be expected to have a regular structure, making decoding particularly challenging. Previous work on decoding edit codes considered the use of side effect machines for decoding, successfully decoding up to 93.86% of error vectors. In this study the recentering/restarting algorithm is used in combination with side effect machines and an alternative representation based upon transpositions. Using the same data as in the previous work, the rate of successful decoding was significantly improved, with many cases obtaining rates very close to 100%.
Keywords :
bioinformatics; GC content; edit metric decoding; quaternary error-correcting codes; recentering-restarting algorithm; sequence data; side effect machines; transposition; Biological cells; Decoding; Genetic algorithms; Sociology; Statistics; Support vector machine classification; Vectors; Bioinformatics; Evolutionary Algorithms; Representation; Sequencing;
Conference_Titel :
Evolutionary Computation (CEC), 2013 IEEE Congress on
Conference_Location :
Cancun
Print_ISBN :
978-1-4799-0453-2
Electronic_ISBN :
978-1-4799-0452-5
DOI :
10.1109/CEC.2013.6557575
