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- Title
SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation.
- Authors
Carlos daMaia, Luciano; Palmieri, Dario Abel; de Souza, Velci Queiroz; Kopp, Mauricio Marini; de Carvalho, Fernando Irajá Félix; de Oliveira, Antonio Costa
- Abstract
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 were performed in a database containing 28 469 nonredundant rice cDNA sequences.
- Subjects
MICROSATELLITE repeats; PLANT genetics; PLANT breeding; NUCLEOTIDE sequence; GENOMIC information retrieval; BIOINFORMATICS
- Publication
International Journal of Plant Genomics, 2008, Vol 2008, p1
- ISSN
1687-5370
- Publication type
Article
- DOI
10.1155/2008/412696