"PolyMin": software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation

dc.contributor.author Frei, Ursula
dc.contributor.author Wollenweber, Bernd
dc.contributor.author Lubberstedt, Thomas
dc.contributor.author Lubberstedt, Thomas
dc.contributor.department Agronomy
dc.date 2018-02-19T00:20:16.000
dc.date.accessioned 2020-06-29T23:03:55Z
dc.date.available 2020-06-29T23:03:55Z
dc.date.copyright Thu Jan 01 00:00:00 UTC 2009
dc.date.issued 2009-06-10
dc.description.abstract <p><h3>Background</h3></p> <p>Analysis of allelic variation for relevant genes and monitoring chromosome segment transmission during selection are important approaches in plant breeding and ecology. To minimize the number of required molecular markers for this purpose is crucial due to cost and time constraints. To date, software for identification of the minimum number of required markers has been optimized for human genetics and is only partly matching the needs of plant scientists and breeders. In addition, different software packages with insufficient interoperability need to be combined to extract this information from available allele sequence data, resulting in an error-prone multi-step process of data handling. <h3>Results</h3></p> <p><em>PolyMin</em>, a computer program combining the detection of a minimum set of single nucleotide polymorphisms (SNPs) and/or insertions/deletions (INDELs) necessary for allele differentiation with the subsequent genotype differentiation in plant populations has been developed. Its efficiency in finding minimum sets of polymorphisms is comparable to other available program packages. <h3>Conclusion</h3></p> <p>A computer program detecting the minimum number of SNPs for haplotype discrimination and subsequent genotype differentiation has been developed, and its performance compared to other relevant software. The main advantages of <em>PolyMin</em>, especially for plant scientists, is the integration of procedures from sequence analysis to polymorphism selection within a single program, including both haplotype and genotype differentiation.</p>
dc.description.comments <p>This article is published as Frei, Ursula K., Bernd Wollenweber, and Thomas Lübberstedt. "" PolyMin": software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation." BMC bioinformatics 10, no. 1 (2009): 176. Doi: <a href="https://doi.org/10.1186/1471-2105-10-176" target="_blank">10.1186/1471-2105-10-176</a>. Posted with permission.</p>
dc.format.mimetype application/pdf
dc.identifier archive/lib.dr.iastate.edu/agron_pubs/276/
dc.identifier.articleid 1267
dc.identifier.contextkey 10950671
dc.identifier.s3bucket isulib-bepress-aws-west
dc.identifier.submissionpath agron_pubs/276
dc.identifier.uri https://dr.lib.iastate.edu/handle/20.500.12876/4616
dc.language.iso en
dc.source.bitstream archive/lib.dr.iastate.edu/agron_pubs/276/2009_Lubberstedt_PolyMin.pdf|||Fri Jan 14 23:07:36 UTC 2022
dc.source.uri 10.1186/1471-2105-10-176
dc.subject.disciplines Agronomy and Crop Sciences
dc.title "PolyMin": software for identification of the minimum number of polymorphisms required for haplotype and genotype differentiation
dc.type article
dc.type.genre article
dspace.entity.type Publication
relation.isAuthorOfPublication 4e4330cd-db15-4ac5-8924-41119139cf32
relation.isOrgUnitOfPublication fdd5c06c-bdbe-469c-a38e-51e664fece7a
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