Additionally, sequences were genotyped by alignment to published HBV sequences of genotypes A to E including the two strains HT and FH which were isolated from patients with FHB (Genbank/EMBL no. M57663, X02763, V00866, E00010, X65257-59, M32138, X02496, V01460, I08805, I27106; L08805 and L27106).
Finally, a random subset of the contigs, which represented a variety of length and read coverage, were validated by direct alignment to previously published, Sanger sequenced, full-length Eucalyptus genes that were directly cloned from cDNA (Additional File 3).
The boundaries of the two rRNAs were tentatively established in our taxa by alignment with published annotated ribosomal RNAs, although the 5′ and 3′ ends were found to be quite divergent among taxa.
Species-specific primers and a TaqMan® probe were designed by alignment of published ribosomal DNA sequences of the second internal transcribed spacer of cyathostomin and Strongylus spp. nematodes.
Two rounds of PCR amplification were carried out with nested pairs of degenerate primers targeting conserved gene regions determined by alignment of published sid-1 homologs from distantly related species (see Additional data file 1) (primer sequences available on request).
Interestingly, the hybridization patterns showed no difference between the two genomes in the two examined fragments, in contrast to the result suggested by alignment of the published genome sequence to the optical map.
The validity of these predictions was further enhanced by comparison, based on multiple alignment and structural information, to published orthologous counterparts.
Protein-coding and ribosomal RNA genes were firstly identified using BLAST searches at GenBank, and then by alignment with previously published mt genomes from species of Crassostrea, Mytilus and other closely related mollusks [ 33].
Both the best-scored whole ITS SATé alignment and the 5.8S re-included SATé alignment produced phylogenetic trees with the highest topological similarity to published multi-gene phylogenies.
All protein-coding, rRNA, and tRNA genes, and intron boundaries within genes in the novel mitochondrial genomes were confirmed by multiple sequence alignment with published red algal data using the T-Coffee package (http://www.tcoffee.org; Di Tommaso et al. 2011).
