Nucleotide sequences of the 13 protein-coding genes were aligned using a perl script on the basis of protein alignments.
Nucleotide alignments of coding sequences were performed on the basis of protein alignments.
On the basis of protein sequence alignment and phylogenetic analysis, it has been suggested that two of these orthologs belong to the barhl1 paralog group (nominated barhl1.1 and barhl1.2) while the third belongs to the barhl2 group [ 6, 12].
To identify which Ser residue in YcgC was most critical for its hydrolase (KDAC) activity, we examined five Ser residues, namely S7, S10, S73, S77, and S200, which are highly conserved among its prokaryotic homologs on the basis of protein sequence alignment.
Then, sample I clusters were analyzed on the basis of codon alignments and sample II on that of protein alignments.
On the basis of the nonredundant protein alignment results, we identified 38 sequence reads that were classified as Henipavirus spp. However, the sequences shared low nucleotide and amino acid identities with known henipaviruses.
As structural alphabet is able to describe local structures of proteins precisely through Protein Blocks approach, conformational similarity has been identified in a substantial number of 'variable' regions in a large data set of protein structural alignments; optimal residue-residue equivalences could be achieved on the basis of Protein Blocks which led to improved local alignments.
Pairwise alignment is the basis of protein sequence comparison methods.
Phylogenetic analysis was performed on the basis of an alignment of protein sequences obtained using MUSCLE [ 53].
The essence of the T-REX approach is in comparison of two trees: a larger gene content tree T, such as the one shown in Figure 1, and a smaller tree constructed on the basis of the alignments of protein sequences from each individual POG (a sequence family tree T sf ).
