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

International journal of plant genomics Pub Date : 2008-01-01 DOI:10.1155/2008/412696

Luciano Carlos da Maia, Dario Abel Palmieri, Velci Queiroz de Souza, Mauricio Marini Kopp, Fernando Irajá Félix de Carvalho, Antonio Costa de Oliveira

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引用次数: 228

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.

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SSR定位器:简单序列重复发现与引物设计和PCR模拟集成的工具。

微卫星或SSRs(简单序列重复)是真核生物中普遍存在的短串联复制。这些序列是植物遗传育种中应用最好的标记技术之一。数据库中丰富的基因组、BAC和EST序列允许对SSR位点的存在和位置进行调查。关于引物序列的其他信息也是植物遗传学家和育种家的目标。在本文中，我们描述了一个整合SSR搜索、基序出现频率和排列、引物设计和PCR模拟与其他数据库的实用程序。该模拟允许在不同扩增序列(即扩增子)之间进行全局比对和同一性和同源性搜索。为了验证该工具的功能，我们在包含28469个非冗余水稻cDNA序列的数据库中进行了SSR发现搜索。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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International journal of plant genomics

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