Database to dynamically aid probe design for virus identification.
Viral infection poses a major problem for public health, horticulture, and animal husbandry, possibly causing severe health crises and economic losses. Viral infections can be identified by the specific detection of viral sequences in many ways. The microarray approach not only tolerates sequence variations of newly evolved virus strains, but can also simultaneously diagnose many viral sequences. Many chips have so far been designed for clinical use. Most are designed for special purposes, such as typing enterovirus infection, and compare fewer than 30 different viral sequences. None considers primer design, increasing the likelihood of cross hybridization to similar sequences from other viruses. To prevent this possibility, this work establishes a platform and database that provides users with specific probes of all known viral genome sequences to facilitate the design of diagnostic chips. This work develops a system for designing probes online. A user can select any number of different viruses and set the experimental conditions such as melting temperature and length of probe. The system then returns the optimal sequences from the database. We have also developed a heuristic algorithm to calculate the probe correctness and show the correctness of the algorithm. (The system that supports probe design for identifying viruses has been published on our web page http://bioinfo.csie.ncu.edu.tw/.)
Lin
Feng-Mao
FM
Department of Computer Science and Information Engineering, National Central University, Jhongli City, Taiwan, ROC. meta@db.csie.ncu.edu.tw
Huang
Hsien-Da
HD
Chang
Yu-Chung
YC
Tsou
Ann-Ping
AP
Chan
Pak-Leong
PL
Wu
Li-Cheng
LC
Tsai
Meng-Feng
MF
Horng
Jorng-Tzong
JT
D000465:Algorithms; D002874:Chromosome Mapping / Q000379:methods; D015342:DNA Probes / Q000235:genetics*; D004279:DNA, Viral / Q000032:analysis* / Q000145:classification / Q000235:genetics*; D030541:Databases, Genetic; D016679:Genome, Viral / Q000235:genetics*; D020411:Oligonucleotide Array Sequence Analysis / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*
D015342:DNA Probes; D004279:DNA, Viral