For subtyping and further analysis, the nucleotide sequence spanning the p24 and p7 region of gag gene, nt 1577 2040, HXB2 [31] (comprising 460 470 bp), was aligned with sequences from the Los Alamos HIV sequence database.
To verify the specificity of RNAi for SeTre-1 and SeTre-2 genes, the dsSeTre-1 fragment (460 bp) was aligned with the dsSeTre-2 fragment (475 bp), and 19-bp consecutive identical sequences between the two fragments were not found (Figure 5A).
HQ336219) of 1,479 bp was aligned with 26 other DENV-3 strains, including the most similar sequences identified in nucleotide BLAST search and a global set of sequences representing different genotypes (4), by using MUSCLE (www.ebi.ac.uk/Tools/muscle/index.html).html
RNA-seq reads of 100 bp were aligned to the genome assembly with the Burrows-Wheeler Alignment tool (BWA) [ 20] in paired-end mode.
RNA-seq reads of 50 bp were aligned against the mouse genome (mm9) references with TopHat2 (Langmead et al, 2009; Trapnell et al, 2009, 2012).
In total, 802,156 high-quality reads with an average read length of 377 bp were aligned against the unigene set.
The lengths of the genomic sequences of the eight non-homeologous PDI-like genes were: 1) TaPDIL2-1: 5213 bp; 2) TaPDIL3-1: 4294 bp; 3) TaPDIL4-1: 3820 bp, 4) TaPDIL5-1: 5326 bp 5) TaPDIL6-1: 2162 bp; 6) TaPDIL7-1: 2887 bp; 7) TaPDIL7-2: 2475 bp; 8) TaPDIL8-1: 7034 bp; they were aligned with the corresponding cDNA sequences to determine the exon-intron structure.
Nucleotide sequences (286 bp) long were aligned with the reference sequences using CLUSTAL W [36]. Phylogenetic relationships were deduced by means of DNADIST-NEIGHBOR from PHYLIP.
In the cytochrome b region, a total of 1120 bp sites were aligned, with 352 parsimony-informative characters.
