String barcoding: uncovering optimal virus signatures

There are many critical situations when one needs to rapidly identify an unidentified pathogen from among a given set of previously sequenced pathogens. DNA or RNA hybridization chips can be designed for such identifications. Each cell in the chip can report the presence or absence of a specific substring of DNA in the unidentified pathogen. Properly designed, the collection of reports obtained from the cells can uniquely identify any pathogen in the set, or determine that the unidentified pathogen is not in the set. There is a limit to the number of cells on a chip, and a range of substring lengths that a cell can handle. So, given the full sequences of a set of pathogens, the problem is to design the chip by selecting the smallest set of substrings of the appropriate lengths, so that each pathogen in the set has a unique set of cells that report a substring. For any given pathogen, the set of reporting cells is its signature, and hence the entire system is a "barcode" syst...

• Type: Conference
• Year: 2002
• Where: RECOMB
• Authors: Sam Rash, Dan Gusfield
• Keywords: Computational Biology, Key Technical Ideas, RECOMB 2002, RNA Hybridization Chips, Unidentified Pathogen