TY - GEN
T1 - An algorithm for mapping short reads to a dynamically changing genomic sequence
AU - Flouri, Tomáš
AU - Holub, Jan
AU - Iliopoulos, Costas S.
AU - Pissis, Solon
PY - 2010/12/1
Y1 - 2010/12/1
N2 - The constant advances in sequencing technology have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads), during a single experiment, and with a much lower cost than previously possible. Due to this massive amount of data, efficient algorithms for mapping these reads to reference sequences are in great demand, and recently, there has been ample work for publishing such algorithms. In this paper, we study a different version of this problem: mapping these reads to a dynamically changing genomic sequence. We propose a new practical algorithm, which employs a suitable data structure that takes into account potential dynamic effects (replacements, insertions, deletions) on the genomic sequence. The presented experimental results demonstrate that the proposed approach can be applied to address the problem of mapping millions of reads to multiple genomic sequences.
AB - The constant advances in sequencing technology have redefined the way genome sequencing is performed. They are able to produce tens of millions of short sequences (reads), during a single experiment, and with a much lower cost than previously possible. Due to this massive amount of data, efficient algorithms for mapping these reads to reference sequences are in great demand, and recently, there has been ample work for publishing such algorithms. In this paper, we study a different version of this problem: mapping these reads to a dynamically changing genomic sequence. We propose a new practical algorithm, which employs a suitable data structure that takes into account potential dynamic effects (replacements, insertions, deletions) on the genomic sequence. The presented experimental results demonstrate that the proposed approach can be applied to address the problem of mapping millions of reads to multiple genomic sequences.
UR - http://www.scopus.com/inward/record.url?scp=79952367059&partnerID=8YFLogxK
UR - http://www.scopus.com/inward/citedby.url?scp=79952367059&partnerID=8YFLogxK
U2 - 10.1109/BIBM.2010.5706551
DO - 10.1109/BIBM.2010.5706551
M3 - Conference contribution
AN - SCOPUS:79952367059
SN - 9781424483075
T3 - Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
SP - 133
EP - 136
BT - Proceedings - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
T2 - 2010 IEEE International Conference on Bioinformatics and Biomedicine, BIBM 2010
Y2 - 18 December 2010 through 21 December 2010
ER -