Voltar
Artigo Acesso aberto Produção Nacional Revisado por pares
BIBTEX RIS

SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation

2008; Hindawi Publishing Corporation; Volume: 2008; Linguagem: Inglês

10.1155/2008/412696

ISSN

1687-5370

Autores

Luciano Carlos da Maia, Darío Abel Palmieri, Velci Queiróz de Souza, Maurício Marini Köpp, Fernando Irajá Félix de Carvalho, Antônio Costa de Oliveira,

Tópico(s)

RNA and protein synthesis mechanisms

Resumo

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.

Referência(s)