The availability of whole genome sequence of B. rapa[ 27] facilitated the design of a 60-mer oligonucleotide microarray platform (62,654 probes targeting 42,162 Brassica genes) based on predicted gene models from the genome sequence.
Gaps in the genome were filled by PCR, based on predicted gene organization in red-lineage plastids.
Activated and inactivated pathways/genes, and activating or inhibitory symbols are based on predicted effects of genome alterations and/or pathway functions.
A recently proposed algorithm, AbundanceBin, introduced another method that bins reads based on predicted abundances of the genomes sequenced.
In contrast, a previous study identified and classified 46 putative serpentine receptors in the P. falciparum genome, based on predicted membrane topology patterns [17].
For mRNA expression analysis, a custom-made Agilent expression array (JHI Solanum tuberosum 60 k v1; ArrayExpress accession A-MEXP-2272 A-MEXP-2272 A-MEXP-2272nscripts of the Solanum tubasedum genone (version 3.4) was used according to the supredicteddirectranscriptsCofor Microarray-Based Gene Expression Analysis Low Inputheuick Amp Labeling v. 6.5; Agilent).
Third, the MITE in P. salinus is present at high copy numbers relative to TEs in other viral genomes and, based on predicted ORFs, some of these copies may have contributed novel protein-coding sequence to the virus.
It is primarily a genome-scale network based on predicted protein-protein interactions and co-expression.
Three different gene specific primers (U1: 5'-ATGAAGACCCTCATCCTGTG-3'-ACAGTACACAGTAATTAGAG-3TTandG-3' anD1b1b: 5'-GGCTGGCAAACGGTATTTCT-3', SIGMA) were designed based on the genome predicted TCPP-1 sequence [GenBank: XM_966374].
MiRDeep analysis was done according to the miRDeep protocol, and a data set of putative precursor sequences was obtained from the genome, based on the predicted mature miRNA alignments.
