GeneMark and NCBI's ORF Finder programs were used to identify open reading frames within the KS10 genome sequence [ 18].
The AMD [ 47], GLAM2 [ 48], Weeder [ 49], and DREME [ 50] programs were used to identify motifs [ 42], and the Tomtom program [ 51] was used to compare standard motif representations in the JASPAR core database [ 52].
Based on the performance comparison of three common computational programs (i.e., PhyloGenie, DarkHorse, and AlienG) in HGT prediction, we recommend that a combination of two or all three programs be used to identify acquired genes.
MACS (Zhang et al, 2008b) and CCAT (Xu et al, 2010) peak-finding programs were used to identify histone-modified regions by comparing both Mbd3-null and parental samples to their respective input DNA controls.
Two programs were used to identify cyclic patterns of expression in FPKM data, COSPOT (which is described in Panda et al. 2002) and an application of the discrete Fourier transform (DFT).
The NNSPLICE (http://www.fruitfly.org/seq_tools/splice.html) [ 14], NetGene2 (http://www.cbs.dtu.dk/services/NetGene2/) [ 15], and GeneSplicer (http://www.cbcb.umd.edu/software/GeneSplicer/gene_spl.shtml) [ 16] programs were used to identify potential splice sites.
For the nonsynonymous variants, PolyPhen-2 [ 24] and SIFT [ 25] programs were used to identify those with predicted deleterious effects as defined by PolyPhen-2 score [Probably damaging, 0.909-1, Possibly damaging 0.447 - 0.908, Benign 0 0.446 (HumVar score)], and SIFT score covered by ANNOVAR LJB2 (Damaging < 0.05, Tolerant ≥ 0.05) [ 26].
Cuffdiff program was used to identify the differentially expressed genes between the CQ-sensitive and resistant strains.
A computer simulation program was used to identify the worst case loading position for the small female head and neck.
Finally, a program was used to identify whether posts contained any opposing content so that all posts could be categorized as either the opposing or supporting type.
