a parallel and incremental algorithm for efficient unique signature discovery on dna databases并行和增量算法高效独特的签名发现dna数据库.pdfVIP

Lee et al. BMC Bioinformatics 2010, 11:132 /1471-2105/11/132 METHODOLOGY ARTICLE Open Access A parallel and incremental algorithm for efficient unique signature discovery on DNA databases Hsiao Ping Lee1,2,3, Tzu-Fang Sheu4*, Chuan Yi Tang3 Abstract 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 signatures of length ≤ l with mismatch tolerance ≥ d. A discovery algorithm that could discover all implicit signatures, such that those that meet the requirements concerning the results, would be more helpful than one that depends on trial and error. However, existing discovery algorithms do not address the need to discover all implicit signatures. Results: This work proposes two discovery algorithms - the consecutive multiple discovery (CMD) algorithm and the parallel and incremental signature discovery (PISD) algorithm. The PISD algorithm is designed for efficiently discovering signatu