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Bioinformatics Advance Access originally published online on June 22, 2007
Bioinformatics 2007 23(16):2155-2162; doi:10.1093/bioinformatics/btm313
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© The Author 2007. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

PowerCore: a program applying the advanced M strategy with a heuristic search for establishing core sets

Kyu-Won Kim 1,2,{dagger}, Hun-Ki Chung 1,{dagger}, Gyu-Taek Cho 1, Kyung-Ho Ma 1, Dorothy Chandrabalan 3, Jae-Gyun Gwag 1, Tae-San Kim 1, Eun-Gi Cho 1 and Yong-Jin Park 1,3,*

1National Institute of Agricultural Biotechnology, 247 Seodun-dong, Suwon, 441-707, 2Qubesoft,R/No, Dongyoung Central B/D, 847-2 Geumjeong-dong, Gunpo 434-050, R.Korea and 3Bioversity International, APO Office, Serdang 43400, Malaysia

*To whom correspondence should be addressed.


  Abstract

Motivation: Core sets are necessary to ensure that access to useful alleles or characteristics retained in genebanks is guaranteed. We have successfully developed a computational tool named ‘PowerCore’ that aims to support the development of core sets by reducing the redundancy of useful alleles and thus enhancing their richness.

Results: The program, using a new approach completely different from any other previous methodologies, selects entries of core sets by the advanced M (maximization) strategy implemented through a modified heuristic algorithm. The developed core set has been validated to retain all characteristics for qualitative traits and all classes for quantitative ones. PowerCore effectively selected the accessions with higher diversity representing the entire coverage of variables and gave a 100% reproducible list of entries whenever repeated.

Availability: PowerCore software uses the .NET Framework Version 1.1 environment which is freely available for the MS Windows platform. The files can be downloaded from http://genebank.rda.go.kr/powercore/. The distribution of the package includes executable programs, sample data and a user manual.

Contact: yjpark{at}rda.go.kr

Associate Editor: Alfonso Valencia

{dagger}The authors wish it to be known that, in their opinion, the first two authors should be regarded as joint First Authors.

Received on February 28, 2007; revised on May 24, 2007; accepted on June 5, 2007

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