The Blast2GO suite [ 39] was used for functional annotation of transcripts applying the function for the mapping of GO terms to transcripts with BLAST hits obtained from BLAST searches against nr.
Instead of applying the function to continuously model the effect of age, cohort and period effect, we preferred a categorical analysis to compare French and Italian BSE epidemics.
This paper develops such a computer-aided design method, under the guide of Axiomatic Design, which can apply the functions of current CAD/CAE software.
Thus, a mathematical expression such as '22' denotes the result of applying the function 2 to the number 2 as argument, namely, the number 4. Similarly, the expression '7 + 1' denotes the result of applying the binary function + to the numbers 7 and 1 as arguments, in that order.
The principal components of the genotypic variance was obtained by applying the prcomp function of R on the SNP data of Schacherer et al. [ 14].
Note that the PDF defined in (2.4) can be easily used to generate a T-X{Y} family of distributions by applying the quantile function of any existing distribution.
Matrix singular value decomposition (SVD) was carried out by conventional methods by applying the svd function of Splus or R to the 2,833×13 (cyclic genes) and the 7,784×13 (all genes) matrices of genes by time-points.
K-means clustering is done by applying the "kmeans" function of R with 'center = 4'.
PCR conditions were optimized by applying the gradient function of the DNA engine Opticon™ 2 (Bio-rad, München, Germany) for HPRT-1 (NM_000194) as housekeeping gene and for COMP.
All obtained motifs were compared to each other by applying the minaligndiff function of the TAMO distribution and when motifs occur with an alignment difference < 0.2, only the motif with the highest Bit score is further considered.
