In the case of SerRS and ThrRS, the respective protein family alignments were subsequently aligned in an additional profile alignment step.
The sequence alignments were subsequently aligned with P. taeda, which was used as an outgroup for each species separately using the profile-profile option in MUSCLE (Edgar 2004).
GSSUs are subsequently aligned and these partial alignments are merged into the final RNA structure alignment and scored.
For each genome, assembly performance was optimized by scanning the best k-mer value from 25to5555. Genome scaffolds were subsequently aligned against database of syntenic alignments from Homo sapiens, Pan troglodytes, and Callit.
Nucleotide sequences of these confirmed arsC genes were aligned according to the amino acid alignment, and the putative arsC ORFs subsequently aligned to these confirmed sequences.
Contigs were assembled using CodonCode aligner Ver2.0.6 (CodonCode Co). and were subsequently aligned by the same software.
Found homologous structures are subsequently aligned with the target protein by a global structural alignment algorithm.
The nucleotide sequences were subsequently aligned by RevTrans[ 54], using the MUSCLE amino acid alignment as a template.
The 136 Tandrs and 1 V1r1 were translated into protein sequences and were subsequently aligned with the MUSCLE program (Edgar 2004), and the resulting alignment was subjected to manual inspection in MEGA6 (Tamura et al. 2013).
Using the protein sequence alignment as a guide, the corresponding nucleotide sequences are subsequently aligned, codon by codon, using pal2nal (Suyama et al. 2006).
The non-mapping reads, which harbor chimeras, were subsequently aligned against the transcriptome returning those reads that had a partial alignment of at least 18 nucleotides.
