We selected nine unigenes that were respectively defined as mdPGRP (LE, SC), mdproPO1, mdPAP (1, 2, 3), and mdSerpin (3, 11) and conducted an alignment to their matched sequences in the RefSeq database of the M. domestica genome (Scott et al. 2014).
To ensure reliable short read alignments base quality scores were taken into account to conduct an interative alignment approach aiming to identify the best mapping position for each read.
We developed scripts, which were used to remove 5' and 3' UTRs from the orthologous pairs and conduct a pairwise alignment in muscle 3.7 [ 103].
Prior to the modeling, we conducted a 3D alignment of 3VRI, 3VRJ, and 3UPR in order to evaluate any significant deviations between the protein structures, bound ligand, and peptides.
To understand this limited recognition we conducted a sequence alignment between HLA-G and other MHC class I molecules and compared the four contact residues responsible for KIR-mediated recognition of MHC class I molecules.
Then, we conducted a multiple alignment of the individual finger motifs from all C2H2-ZNF genes, to then determine if the similar finger motifs from a given C2H2-ZNF gene group together.
To refine the number of predicted target genes for the 59 differentially expressed miRNAs, we conducted a parallel alignment analysis between the list of predicted genes and the list of stage-specific genes identified by genome-wide transcript expression profiling.
Given that R174K mutation was not a unique sequence feature of axolotl p53, we conducted a sequence alignment of the p53 from several vertebrates spanning mammals to fish (human, mouse, rat, Spalax, chicken, axolotl, Xenopus, barbel & zebrafish) to identify the changes in table- 2 that are unique to the axolotl p53.
We conducted a multiple alignment for all the analyzed sequences to investigate the domain conservation in PL10, DDX3X and DDX3Y, and found that the DEAD/DEAH box helicase domain (Pfam: PF00270) and helicase conserved C-terminal domain (Pfam: PF00271) of the DDX3 genes are highly conserved [Additional File 3].
To analyze L1PA7 and L1P3 expansion in the NWM genomes, we initially selected L1PA7 elements with intact open reading frame 2 (Oregionsginns in all of the primate genomes, and we conducted a multiple alignment of DNA sequences of their ORF2 regions using CLUSTALW2 (parameters: -type=dna -quicktree).
We conducted a RADICAL analysis using an alignment of 13 cyanobacterial genomes provided by Shi and Falkowski (2008).
