TY - GEN
T1 - Practical and efficient algorithms for degenerate and weighted sequences derived from high throughput sequencing technologies
AU - Antoniou, Pavlos
AU - Iliopoulos, Costas S.
AU - Mouchard, Laurent
AU - Pissis, Solon P.
PY - 2009/11/26
Y1 - 2009/11/26
N2 - High throughput, (or next generation) sequencing technologies have opened new and exciting opportunities in the use of DNA sequences. The new emerging technologies mark the beginning of a new era of high throughput short read sequencing: they have the potential to assemble a bacterial genome during a single experiment and at a moderate cost. In this paper, we address the problem of efficiently mapping millions of degenerate and weighted sequences to a reference genome with respect to whether they occur exactly once in the genome or not, and by taking probability scores into consideration. In particular, we define and solve the Massive Exact and Approximate Unique Pattern Matching problem for degenerate and weighted sequences derived from high throughput sequencing technologies.
AB - High throughput, (or next generation) sequencing technologies have opened new and exciting opportunities in the use of DNA sequences. The new emerging technologies mark the beginning of a new era of high throughput short read sequencing: they have the potential to assemble a bacterial genome during a single experiment and at a moderate cost. In this paper, we address the problem of efficiently mapping millions of degenerate and weighted sequences to a reference genome with respect to whether they occur exactly once in the genome or not, and by taking probability scores into consideration. In particular, we define and solve the Massive Exact and Approximate Unique Pattern Matching problem for degenerate and weighted sequences derived from high throughput sequencing technologies.
UR - http://www.scopus.com/inward/record.url?scp=70450183215&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=70450183215&partnerID=8YFLogxK
U2 - 10.1109/IJCBS.2009.48
DO - 10.1109/IJCBS.2009.48
M3 - Conference contribution
AN - SCOPUS:70450183215
SN - 9780769537399
T3 - Proceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009
SP - 174
EP - 180
BT - Proceedings - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009
T2 - 2009 International Joint Conference on Bioinformatics, Systems Biology and Intelligent Computing, IJCBS 2009
Y2 - 3 August 2009 through 5 August 2009
ER -