Several well-established sequence comparison algorithms are based on sequence alignment: they compute sequence similarity by aligning portions of sequences (e.g., subsequences) that have common nucleotide assignments.
HGT detection has been pursued by phylogenetic methods, based on sequence alignment, and by composition-based methods that involve alignment-free features such as G + C content, synonymous codon usage (SCU) and the frequencies of overlapping short oligomers.
The resulting Ger receptor protein sequences were then clustered by neighbor-joining based on sequence alignment.
Based on sequence alignment, four primers were designed amplifying the M gene of type II PRRSV and were subsequently utilized in an RT-LAMP assay.
Based on sequence alignment and structural modeling, a library of enzyme variants was created by a semi-rational evolution strategy in position Thr238 and Pro242.
In re-sequencing studies, where a high-quality reference genome exists, the reads from the machine are mapped to the reference genome based on sequence alignment, which in turn is used for calling variants.
This tree, as expected, showed marked differences from the known kinome tree based on sequence alignment [4].
We overlaid the potential protonation sites of the VMATs or VAChT on the structure of ecMdfA based on sequence alignment (Fig. S1).
Based on sequence alignment and homology modelling, we were able to provide mechanistic insights into the association between the inhibition and the conformational changes of these transporters.
Based on sequence alignment, three residues were chosen for site-directed mutagenesis to obtain two single mutants (K312E and E539K) and two double mutants (T166A/E539K and K312E/E539K).
Based on sequence alignment of Bbp, SdrG and ClfA (Davis et al., 2001; Josefsson et al., 1998), we engineered a plasmid that would generate a recombinant fusion protein covering residues Asn273 Pro598 of Bbp from S. aureus, a segment containing both N2 and N3 domains (Fig. 1A), with N-terminal GST-tag for purification purposes in Escherichia coli.
