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Nucleic Acids Research 2006 34(4):e31; doi:10.1093/nar/gnj030
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Published online 21 February 2006

© The Author 2006. Published by Oxford University Press. All rights reserved
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use, please contact journals.permissions{at}oxfordjournals.org

Methods Online

New softwares for automated microsatellite marker development

Wellington Martins, Daniel de Sousa1, Karina Proite2, Patrícia Guimarães2, Marcio Moretzsohn2 and David Bertioli3

Department of Computer Science, Catholic University of Goiás Brazil 1Department of Computer Science, Catholic University of Rio de Janeiro Brazil 2Embrapa Genetic Resources and Biotechnology, Brasília Brazil 3Genomic Sciences and Biotechnology, Catholic University of Brasília Brazil

*To whom correspondence should be addressed. Tel: +55 62 32271381; Fax: +55 62 32271073; Email: wsmartins{at}ucg.br

Received November 23, 2005. Revised January 31, 2006. Accepted January 31, 2006.

Microsatellites are repeated small sequence motifs that are highly polymorphic and abundant in the genomes of eukaryotes. Often they are the molecular markers of choice. To aid the development of microsatellite markers we have developed a module that integrates a program for the detection of microsatellites (TROLL), with the sequence assembly and analysis software, the Staden Package. The module has easily adjustable parameters for microsatellite lengths and base pair quality control. Starting with large datasets of unassembled sequence data in the form of chromatograms and/or text data, it enables the creation of a compact database consisting of the processed and assembled microsatellite containing sequences. For the final phase of primer design, we developed a program that accepts the multi-sequence ‘experiment file’ format as input and produces a list of primer pairs for amplification of microsatellite markers. The program can take into account the quality values of consensus bases, improving success rate of primer pairs in PCR. The software is freely available and simple to install in both Windows and Unix-based operating systems. Here we demonstrate the software by developing primer pairs for 427 new candidate markers for peanut.

Correspondence may also be addressed to David Bertioli. Tel: +55 61 34484735; Fax: +55 61 33403658; Email: david{at}pos.ucb.br


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