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Commissioned in 2012, the consultants produced a plan through the year 2030 by first mapping the regional drainage area; second, creating computer analyses and models to evaluate and simulate present and future conditions; and third, making recommendations for a reconstruction plan that prioritized the necessity of repairs and assessing the technical and financial aspects of future developments.
The pi and crasiRNA pools were annotated by first mapping the pools to the Meug_2.0 tammar genome assembly as described in the small RNA mapping section.
The genes in the RNA-seq data set were mapped to the Entrez IDs in the gene sets by first mapping the RNA-seq Ensembl gene IDs to Entrez IDs.
The SVM algorithm operates by first mapping the training set into a high-dimensional feature space and then attempting to locate in that space a hyperplane that separates positive from negative examples.
The locus specific gene expression data analysis was done by first mapping the Affymetrix probe sets to their corresponding genes in the mouse genome in Ensembl database version 43.
SNPs were identified by first mapping the filtered reads to the final meta-assembly using BWA v0.7.10 [ 103] and then mpileup of SAMtools v1.1 [ 104] was used to detect SNP sites.
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To this end, we analyzed the 1,999 MPH-correlated genes from Thiemann et al.[ 11] for possible co-localization with known heterotic QTL for GY, by first mapping those genes to the B73 maize genome followed by distribution analysis.
We performed an independent search for Hfq-dependent sRNAs by first mapping all the Rho-independent terminators located within intergenic regions, and then identifying sRNAs by detecting short-length transcriptional activity upstream of any of these terminators.
To test this, we analysed the smaller negatively correlated 34 gene set by first mapping each of the 34 transcripts to the Arabidopsis proteome, to identify homologous gene loci and selected those with E-value scores of 1 × 10 -10 or less.
Deletions in the B. neohumeralis or B. jarvisi genomes (with respect to the B. tryoni assembly) were identified by first mapping reads from the two other species to the B. tryoni assembly using bwa-mem, which allows gapped alignments.
To take the presence of Rho-independent terminator into consideration and to ensure that all the sRNAs with Rho-independent terminators are identified, we performed a second search by first mapping all of the Rho-independent terminators in the E. amylovora genome, and then identifying sRNA-encoding genes by detecting short-length transcriptional activity upstream of the terminators.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com