Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT

doi:10.1186/1471-2164-9-356

BMC Genomics
Volume 9

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Neigenfind J
Gyetvai G
Basekow R
Diehl S
Achenbach U
Gebhardt C
Selbig J
Kersten B

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Neigenfind J
Gyetvai G
Basekow R
Diehl S
Achenbach U
Gebhardt C
Selbig J
Kersten B
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Haplotype inference from unphased SNP data in heterozygous polyploids based on SAT

Jost Neigenfind¹^,2 , Gabor Gyetvai³ , Rico Basekow¹^,2 , Svenja Diehl² , Ute Achenbach³ , Christiane Gebhardt³ , Joachim Selbig⁴ and Birgit Kersten¹^,2

¹Bioinformatics, GabiPD team, Max Planck Institute of Molecular Plant Physiology, 14424 Potsdam-Golm, Germany

²Bioinformatics, Former RZPD German Resource Center for Genome Research GmbH, Heubnerweg 6, D-14059, Berlin, Germany

³Max Planck Institute for Plant Breeding Research, Carl von Linnè Weg 10, 50829 Köln, Germany

⁴Institute of Biochemistry and Biology, University of Potsdam, c/o MPI-MP, 14424 Potsdam, Germany

author email corresponding author email

BMC Genomics 2008, 9:356doi:10.1186/1471-2164-9-356


Published:	30 July 2008

Additional files

Additional file 1:

Computational haplotype inference – XML output of SATlotyper. The XML output of SATlotyper is based on the treelike structure of the result. The root of the tree is marked by the <result> tag. The next level in the tree consists of the original input data (<source>), the scored haplotype (<haplotype>) list derived by bootstrapping (<bootstrapping>) and the calculated alternative inferences of the unphased input data (<haplotypings>). The haplotypings branch contains at least one inference of the original input data (<haplotyping>) with the corresponding most parsimonious set of haplotypes (<haplotypes>) and phased genotypes (<genotypes>) as subelements where a genotype (<genotype>) contains the ploidy-specific number of inferred haplotypes.

Format: XML Size: 798KB Download file

Additional file 2:

Experimental methods. This file describes the experimental methods used for (i) the generation of unphased SNP data from tetraploid potato individuals and (ii) the analysis of haplotype inference by amplicon cloning and sequencing.

Format: PDF Size: 54KB Download file

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