TY - GEN
T1 - Imposed constraints on the smith-waterman alignment algorithm for enhanced modeling of a single-molecule DNA sequencer
AU - Humphrey, Patrick G.
AU - Bashford, Gregory R.
PY - 2005
Y1 - 2005
N2 - 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.
AB - 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.
UR - http://www.scopus.com/inward/record.url?scp=33947106398&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=33947106398&partnerID=8YFLogxK
M3 - Conference contribution
AN - SCOPUS:33947106398
SN - 0780392329
SN - 9780780392328
T3 - 2005 IEEE International Conference on Electro Information Technology
BT - 2005 IEEE International Conference on Electro Information Technology
T2 - 2005 IEEE International Conference on Electro Information Technology
Y2 - 22 May 2005 through 25 May 2005
ER -