Selection of optimal DNA oligos for gene expression arrays

Li, Fugen; Stormo, Gary D.

doi:10.1093/bioinformatics/17.11.1067

Cited by 204 publications

(132 citation statements)

References 23 publications

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“…The length of the probes designed by existing software ranges from 20 to 70: around 20 (Lockhart et al, 1996;Li and Stormo, 2001;Kaderali and Schliep, 2002;Sung and Lee, 2003;Tolonen et al, 2002), around 30 (Kaderali and Schliep, 2002;Rahmann, 2002) around 50 (Li and Stormo, 2001;Sung and Lee, 2003;Rouillard et al, 2003), and around 70 (Li and Stormo, 2001;Sung and Lee, 2003;Wright and Church, 2002;Bozdech et al, 2003). Our software is able to design probes of various length in this range (see Section 3.2).…”

Section: Our Resultsmentioning

confidence: 99%

“…The quantitative criteria they proposed are widely used (Li and Stormo, 2001;Relogio et al, 2002;Tolonen et al, 2002;Sung and Lee, 2003;Rouillard et al, 2003;Bozdech et al, 2003), with some minor variations. Homogeneity and specificity were also used in their algorithm, though the exact algorithm has not been published.…”

Section: Previous Workmentioning

confidence: 99%

“…It is generally agreed that T m and free energy can be used as parameters to evaluate probe hybridization behavior and have been shown to be useful (Li and Stormo, 2001). 3 As for specificity, there are two major measurements: Hamming distance (Li and Stormo, 2001;Rahmann, 2002;Sung and Lee, 2003) and BLAST search (Relogio et al, 2002;Tolonen et al, 2002;Rouillard et al, 2003;Wright and Church, 2002;Bozdech et al, 2003). Using BLAST (Altschul et al, 1997) (http://www.ncbi.nih.gov/blast/), the algorithms assume the search is done in advance and the results passed as input.…”

Section: Previous Workmentioning

confidence: 99%

“…MFOLD (Zuker et al, 1999), Vienna RNAfold (Hofacker, 2003) and Smith-Waterman (Smith and Waterman, 1981) algorithms have been used in Bozdech et al (2003), Rouillard et al (2003), Matveeva et al (2003), Wright and Church (2002) for this purpose. 4 Other algorithms (Li and Stormo, 2001;Tolonen et al, 2002;Relogio et al, 2002;Sung and Lee, 2003;Rahmann, 2002) directly check sensitivity by eliminating probes that are self-complementary.…”

Section: Previous Workmentioning

confidence: 99%

“…Li and Stormo (2001) used a fast approximate matching search algorithm Myersgrep (Myers, 1950) for uniqueness checking. However, the algorithm is still not fast enough for computing probes of large genome sets.…”

Section: Previous Workmentioning

confidence: 99%

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Randomized probe selection algorithm for microarray design

Gąsieniec

Sant

et al. 2007

Journal of Theoretical Biology

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DNA microarray technology, originally developed to measure the level of gene expression, has become one of the most widely used tools in genomic study. The crux of microarray design lies in how to select a unique probe that distinguishes a given genomic sequence from other sequences. Due to its significance, probe selection attracts a lot of attention. Various probe selection algorithms have been developed in recent years. Good probe selection algorithms should produce a small number of candidate probes. Efficiency is also crucial because the data involved are usually huge. Most existing algorithms are usually not sufficiently selective and quite a large number of probes are returned. We propose a new direction to tackle the problem and give an efficient algorithm based on randomization to select a small set of probes and demonstrate that such a small set of probes is sufficient to distinguish each sequence from all the other sequences. Based on the algorithm, we have developed probe selection software RANDPS, which runs efficiently in practice. The software is available on our website (http://www.csc.liv.ac.uk/$cindy/RandPS/RandPS.htm). We test our algorithm via experiments on different genomes (Escherichia coli, Saccharamyces cerevisiae, etc.) and our algorithm is able to output unique probes for most of the genes efficiently. The other genes can be identified by a combination of at most two probes.

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