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For the initial construction of the reference transcriptome Velvet [ 58] was used.
Second, we investigated the optimal construction of the reference population when the number of phenotypic records is limited.
constructMetabolicNetwork is used for construction of the reference metabolic network based on the metabolic reaction relationships in KEGG metabolic pathway dataset.
Individuals from a nondiapausing USDA-reared WCR colony were also obtained during 2009; their RNA was used only for construction of the reference transcriptome.
During the construction of the reference network, the information whether the interacting genes are expressed in the same tissue is ignored.
For the construction of the reference clusters, genomic sequences for these species were also downloaded [ C.elegans genome build Ce6, S.bicolor genome (Sbi1) and O.sativa ssp. Indica (Gramene build Jan 2005, 48)].
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The construction of the current reference is based on the positive component detection of the grid voltage.
The construction of the optimum reference set is coded in the select.reference.set function of the ExomeDepth package.
These probes were selected from those used in the construction of the Prunus reference map [ 14] to be single-copy and covering the whole genome at approximately even distances of 10 25 cM.
Because this is a gene-based map, we expect that it will help in the construction of the pine reference sequence that is currently being generated while facilitating other basic and applied research efforts that use a high-density, gene-rich genetic maps.
The first step in the original implementation of the AGSNP pipeline was the construction of a reference sequence and the identification of single-copy sequences in it.
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