Sentence examples for implemented in the genome from inspiring English sources

The raw data from microarray were pre-processed through three steps: background correction was performed, the data were then log-transformed to log2 scale, and normalized by the quantile normalization method implemented in the Genome Studio software (Illumina Inc.).

Data were analyzed using the mixed linear model (MLM) in efficient mixed-model association (EMMA) as implemented in the genome association and prediction integrated tool (GAPIT) in R (Lipka et al. 2012) using a marker-based kinship matrix derived within GAPIT from a subset of 927 markers giving a minimum inter-marker distance of 1 cM.

The latter methodology, sequencing-by-synthesis, is implemented in the Genome Sequencer GS-FLX System (454 Life Sciences), which produces several hundred thousand DNA reads of at least 200 bp; this is done by monitoring the release of pyrophosphate during the growth of a DNA chain driven by a DNA polymerase [ 6].

Orthologs of TFs were identified by a procedure based on the analysis of phylogenetic trees for protein domains in MicrobesOnline [ 54] and validated by bidirectional genome-wide similarity searches with 30% of identity threshold using the Smith-Waterman algorithm implemented in the Genome Explorer program [ 58].

Second, we use the method of Yang et al. (2010) as implemented in the Genome-wide Complex Trait Analysis (GCTA) software (Yang et al. 2011).

A LMM is used to estimate the PVE by measured SNPs for a phenotype, as implemented in the Genome-wide Complex Trait Analysis (GCTA) software package (Yang et al. 2011).

Using this strategy, 64 loci of putative Daphnia ABC genes were identified, for 48 of which evidence of mRNA expression was present in EST databases implemented in the JGI genome portal and wFeaBase (10,392 assembled cDNA on genome scaffolds) (Table 1).

GO analysis was performed using the GO-Slim Mapper tool implemented in the Saccharomyces Genome Database (http://yeastgenome.org/cgi-bin/GO/goSlimMapper.pl).

The phylogenetic profiling developed by Pellegrini et al. (1999) has been implemented in the Plasmodium Genome Resource Database (www.plasmodb.org) but no proteins with profiles significantly similar to PF13_0289 have yet been identified.

One such variant involving 1-monotonous alignments was implemented in the context of genome-to-genome alignments (Brudno et al., 2003).

For overlap alignment, we compared OPTIMA-Overlap with an overlap-finding extension of Gentig v.2 (implemented in the commercial software Genome-Builder from OpGen, which contains a module called SCAFFOLDEXTENDER) [ 17, 24], as well as with Valouev's likelihood-overlap method [ 13].