TY - GEN
T1 - Optimal probing patterns for sequencing by hybridization
AU - Tsur, Dekel
PY - 2006/1/1
Y1 - 2006/1/1
N2 - Sequencing by Hybridization (SBH) is a method for reconstructing a DNA sequence based on its k-mer content. This content, called the spectrum of the sequence, can be obtained from hybridization with a universal DNA chip. The main shortcoming of SBH is that it reliably reconstructs only sequences of length at most square root of the size of the chip. Frieze et al. [9] showed that by using gapped probes, SBH can reconstruct sequences with length that is linear in the size of the chip. In this work we investigate the optimal placement of the gaps in the probes, and give an algorithm for finding nearly optimal gap placement. Using our algorithm, we obtain a chip design which is more efficient than the chip of Frieze et al.
AB - Sequencing by Hybridization (SBH) is a method for reconstructing a DNA sequence based on its k-mer content. This content, called the spectrum of the sequence, can be obtained from hybridization with a universal DNA chip. The main shortcoming of SBH is that it reliably reconstructs only sequences of length at most square root of the size of the chip. Frieze et al. [9] showed that by using gapped probes, SBH can reconstruct sequences with length that is linear in the size of the chip. In this work we investigate the optimal placement of the gaps in the probes, and give an algorithm for finding nearly optimal gap placement. Using our algorithm, we obtain a chip design which is more efficient than the chip of Frieze et al.
UR - http://www.scopus.com/inward/record.url?scp=33750267860&partnerID=8YFLogxK
U2 - 10.1007/11851561_34
DO - 10.1007/11851561_34
M3 - Conference contribution
AN - SCOPUS:33750267860
SN - 3540395830
SN - 9783540395836
T3 - Lecture Notes in Computer Science (including subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics)
SP - 366
EP - 375
BT - Algorithms in Bioinformatics - 6th International Workshop, WABI 2006, Proceedings
PB - Springer Verlag
T2 - 6th International Workshop on Algorithms in Bioinformatics, WABI 2006
Y2 - 11 September 2006 through 13 September 2006
ER -