Database to dynamically aid probe design for virus identification

Feng Mao Lin, Hsien Da Huang, Yu Chung Chang, Ann Ping Tsou, Pak Leong Chan, Li Cheng Wu, Meng Feng Tsai, Jorng Tzong Horng

Research output: Contribution to journalArticlepeer-review

8 Scopus citations

Abstract

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/.)

Original languageEnglish
Pages (from-to)705-713
Number of pages9
JournalIEEE Transactions on Information Technology in Biomedicine
Volume10
Issue number4
DOIs
StatePublished - Oct 2006

Keywords

  • Database
  • Probe design
  • Virus identification

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