Fast and accurate probe selection algorithm for large genomes

@inproceedings{citeulike:1676484, abstract = {The oligo microarray (DNA chip) technology in recent years has a significant impact on genomic study. Many fields such as gene discovery, drug discovery, toxicological research and disease diagnosis, will certainly benefit from its use. A microarray is an orderly arrangement of thousands of DNA fragments where each DNA fragment is a probe (or a fingerprint) of a gene/cDNA. It is important that each probe must uniquely associate with a particular gene/cDNA. Otherwise, the performance of the microarray will be affected. Existing algorithms usually select probes using the criteria of homogeneity, sensitivity, and specificity. Moreover, they improve efficiency employing some heuristics. Such approaches reduce the accuracy. Instead, we make use of some smart filtering techniques to avoid redundant computation while maintaining the accuracy. Based on the new algorithm, optimal short (20 bases) or long (50 or 70 bases) probes can be computed efficiently for large genomes.}, author = {Sung, W. K. and Lee, W. H. }, booktitle = {Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE}, citeulike-article-id = {1676484}, journal = {Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE}, keywords = {string-matching, unique-oligonucleotides}, pages = {65--74}, posted-at = {2007-09-19 16:59:08}, priority = {2}, title = {Fast and accurate probe selection algorithm for large genomes}, url = {http://ieeexplore.ieee.org/xpls/abs\_all.jsp?arnumber=1227305}, year = {2003} }

TY - CONF ID - citeulike:1676484 L3 - citeulike-article-id:1676484 TI - Fast and accurate probe selection algorithm for large genomes T2 - Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE JF - Bioinformatics Conference, 2003. CSB 2003. Proceedings of the 2003 IEEE SP - 65 EP - 74 N2 - The oligo microarray (DNA chip) technology in recent years has a significant impact on genomic study. Many fields such as gene discovery, drug discovery, toxicological research and disease diagnosis, will certainly benefit from its use. A microarray is an orderly arrangement of thousands of DNA fragments where each DNA fragment is a probe (or a fingerprint) of a gene/cDNA. It is important that each probe must uniquely associate with a particular gene/cDNA. Otherwise, the performance of the microarray will be affected. Existing algorithms usually select probes using the criteria of homogeneity, sensitivity, and specificity. Moreover, they improve efficiency employing some heuristics. Such approaches reduce the accuracy. Instead, we make use of some smart filtering techniques to avoid redundant computation while maintaining the accuracy. Based on the new algorithm, optimal short (20 bases) or long (50 or 70 bases) probes can be computed efficiently for large genomes. KW - string-matching KW - unique-oligonucleotides AU - Sung, WK AU - Lee, WH PY - 2003/// UR - http://ieeexplore.ieee.org/xpls/abs_all.jsp?arnumber=1227305 ER -