Title :
Modeling and base-calling for Dna Sequencing-By-Synthesis
Author :
Eltoukhy, Helmy ; El Gamal, Abbas
Author_Institution :
Dept. of Electr. Eng., Stanford Univ., CA
Abstract :
The process of DNA sequencing-by-synthesis and its non-idealities are modeled as a noisy switched linear system parameterized by the unknown DNA sequence. The base-calling problem is then formulated as a parameter detection problem. As this system can have long memory, performing exact maximum-likelihood decoding is computationally prohibitive. An approximate ML method applied to experimental Pyrosequencing data demonstrates reliable read lengths exceeding 200 bases, which is significantly longer than that achieved by current methods
Keywords :
DNA; maximum likelihood decoding; DNA sequencing-by-synthesis; Pyrosequencing data; base-calling problem; maximum-likelihood decoding; noisy switched linear system; parameter detection problem; Bioinformatics; Costs; DNA; Genomics; Linear systems; Maximum likelihood decoding; Maximum likelihood detection; Sequences; System testing; Throughput;
Conference_Titel :
Acoustics, Speech and Signal Processing, 2006. ICASSP 2006 Proceedings. 2006 IEEE International Conference on
Conference_Location :
Toulouse
Print_ISBN :
1-4244-0469-X
DOI :
10.1109/ICASSP.2006.1660522
