A parallel and incremental algorithm for efficient unique signature discovery on DNA databases

Background: DNA signatures are distinct short nucleotide sequences that provide valuable information that is used for various purposes, such as the design of Polymerase Chain Reaction primers and microarray experiments. Biologists usually use a discovery algorithm to find unique signatures from DNA databases, and then apply the signatures to microarray experiments. Such discovery algorithms require to set some input factors, such as signature length l and mismatch tolerance d, which affect the discovery results. However, suggestions about how to select proper factor values are rare, especially when an unfamiliar DNA database is used. In most cases, biologists typically select factor values based on experience, or even by guessing. If the discovered result is unsatisfactory, biologists change the input factors of the algorithm to obtain a new result. This process is repeated until a proper result is obtained. Implicit signatures under the discovery condition (l, d) are defined as the s...

• Type: Journal
• Year: 2010
• Where: BMCBI
• Authors: Hsiao Ping Lee, Tzu-Fang Sheu, Chuan Yi Tang
• Keywords: Algorithm, BMCBI 2010, Discovery Algorithms, Signatures