Biological Systems Engineering
Date of this Version
2005
Document Type
Article
Citation
2005 IEEE International Conference on Electro Information Technology,
DOI: 10.1109/EIT.2005.1627002
Abstract
An effort has been underway to develop a system for de novo sequencing of single DNA molecules with very long reads. The system operates by optically detecting the passage of fluorescently tagged DNA bases through a detection zone. A successful system would be revolutionary with respect to speed, read length, cost and minimized laboratory infrastructure. An important part of system development is modeling of the detection process. In particular, predicting the expected error from a set of sequencing parameters is helpful in system design. This paper describes variations on the Smith-Waterman algorithm for subsequence alignment used in a single-molecule detection model. The alignment algorithm is used to check the modeled output sequence generated from a known input sequence. Variations based on reasonable assumptions led to over an order of magnitude improvement in alignment speed.
Included in
Biochemistry, Biophysics, and Structural Biology Commons, Bioinformatics Commons, Health Information Technology Commons, Other Analytical, Diagnostic and Therapeutic Techniques and Equipment Commons, Systems and Integrative Physiology Commons
Comments
Copyright 2005 IEEE. Used by permission.