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

Date
2009-06-10
Authors
Frei, Ursula
Wollenweber, Bernd
Lubberstedt, Thomas
Lubberstedt, Thomas
Major Professor
Advisor
Committee Member
Journal Title
Journal ISSN
Volume Title
Publisher
Altmetrics
Authors
Research Projects
Organizational Units
Agronomy
Organizational Unit
Journal Issue
Series
Department
Agronomy
Abstract

Background

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.

Results

PolyMin, 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.

Conclusion

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 PolyMin, 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.

Comments

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: 10.1186/1471-2105-10-176. Posted with permission.

Description
Keywords
Citation
DOI
Collections