An application of genetic algorithm to DNA sequencing by oligonucleotide hybridization

Douzono, H.; Hara, Shigeomi; Noguchi, Yoshio

doi:10.1109/ijsis.1998.685424

Cited by 9 publications

(2 citation statements)

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“…A DNA chip comprised of longer probes can be applied to determine longer target sequences, but the number of probes increases at an exponential rate with probe length. To determine the DNA sequences longer than 1000bp, the DNA chip comprised of probes which are longer than 8bp is desirable [4] and it needs about 3oooO (about (48/2) ) probes. Fon longer sequences, we will need the chip comprised of longer probes.…”

Section: Introductionmentioning

confidence: 99%

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A design method of DNA chips using hierarchical self-organizing maps

Douzono

Tokushima

Hara

et al. 2002

Proceedings of the 9th International Conference on Neural Information Processing, 2002. ICONIP '02.

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In this paper, we introduce a design method of DNA chips using Self Organizing Maps(S0M) and Hierarchical SelfOrganizing Maps(H-SOM). DNA chips are powerful tools for sequencings and SNP(Sing1e Nucleotide Polymorphism) analyses of DNA sequences. A DNA chip is an array of DNA probes which can be hybridized with complement subsequences in the target sequence. However, conventional DNA chips are showing tendency to be comprised of large number of long probes and get large in size to achieve high resolution. To shrink the size of DNA chips, design method is considered to be important. To solve this problem, we applied SOM to extract common features of DNA sequences using proper number of probes which efficiently cover the target sequence with sufficient resolutions. Furthermore, H-SOM can design the chip comprised of long probes more efficiently than SOM can. We have designed some DNA chips from the sequence data in genome database using our SOM and H-SOM algorithm and evaluated the chips by computer simulations of SNP analyses.

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Section: Introductionmentioning

confidence: 99%

“…Some works applying SOM to the analysis of DNA sequences were reported [4] and they used SOMs to analyze the relations between genes and their functions. We applied SOMs to find typical probes which were sufficient to represent the target sequences with extracting features of DNA sequences.…”

Section: Introductionmentioning

confidence: 99%