Introduction

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.

Publications

  1. SSR Locator: Tool for Simple Sequence Repeat Discovery Integrated with Primer Design and PCR Simulation.
    Cite this
    da Maia LC, Palmieri DA, de Souza VQ, Kopp MM, de Carvalho FI, Costa de Oliveira A, 2008-01-01 - International journal of plant genomics

Credits

  1. Luciano Carlos da Maia
    Developer

  2. Dario Abel Palmieri
    Developer

  3. Velci Queiroz de Souza
    Developer

  4. Mauricio Marini Kopp
    Developer

  5. Fernando Irajá Félix de Carvalho
    Developer

  6. Antonio Costa de Oliveira
    Investigator

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Summary
AccessionBT000335
Tool TypeApplication
Category
PlatformsWindows
Technologies
User InterfaceTerminal Command Line
Download Count0
Submitted ByAntonio Costa de Oliveira