ssr locator tool for simple sequence repeat discovery integrated with primer design and pcr simulationssr定位器工具简单序列重复发现与引物设计和集成pcr模拟.pdfVIP

Hindawi Publishing Corporation International Journal of Plant Genomics Volume 2008, Article ID 412696, 9 pages doi:10.1155/2008/412696 Resource Review SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation Luciano Carlos da Maia,1 Dario Abel Palmieri,2 Velci Queiroz de Souza,1 Mauricio Marini Kopp,1 ´ ´ 1 1 Fernando Iraja Felix de Carvalho, and Antonio Costa de Oliveira 1 Plant Genomics and Breeding Laboratory, Eliseu Maciel School of Agronomy, Federal University of Pelotas, Pelotas, RS 96.001-970, Brazil 2 Laboratory for Environmental Studies, Catholic University of Salvador, Salvador, BA, 40.220-140, Brazil Correspondence should be addressed to Antonio Costa de Oliveira, acostol@.br Received 5 October 2007; Revised 29 January 2008; Accepted 20 May 2008 Recommended by Chunguang Du Microsatellites or SSRs (simple sequence repeats) are ubiquitous short tandem duplications occurring in eukaryotic organisms. These sequences are among the best marker technologies applied in plant genetics and breeding. The abundant genomic, BAC, and EST sequences available in databases allow the survey regarding presence and location of SSR loci. Additional information concerning primer sequences is also the target of plant geneticists and breeders. In this paper, we describe a utility that integrates SSR searches, frequency of occurrence of motifs and arrangements, primer design, and PCR simulation against other databases. This simulation allows the performance of global alignments and identity and homology searches between different amplified sequences, that is, amplicons. In order to validate the tool functions, SSR discovery searches wer