In the case of DLPs, which exhibit extremely low-alignment error using traditional processing (Henderson et al., 2011), increasing the SNR at low and intermediate resolutions would not be expected to lead to improved alignment.
In order to avoid aligning sequences with an extremely low level of similarity, pairwise alignments were firstly made with the SWG program using data from the mouse and other species with default parameters.
Alignment at regions with extremely low sequence identity was manually adjusted based on the heuristic knowledge that cysteine residues should be well conserved and aligned among homologous extracellular domains.
This typing method was developed to overcome the difficulty of managing wsp nucleotide sequences, which are highly variable in length and show extremely low homology at the four HVRs, thus making alignment reconstructions impracticable (see example in Fig. 1B).
This happened when the Ks was extremely low or when there were no substitution in the alignment (i.e. 100 % match), respectively.
At first glance the extremely low π value around window midpoint position 121 in the total alignment may be surprising because this low local variation is not reflected in the consensus alignment to that extreme.
Indeed, when performing an all-AA residue alignment, 3VRI has a 96% overlay similarity with 3VRJ and an extremely low pairwise RMSD equal to 0.15 Å (see Fig. 3).
BLAST hits with extremely low e-values (1e-30 or lower) and high query coverage were then aligned with either MUSCLE (Edgar 2004) or ClustalW (Thompson et al. 2002) to compare alignments and verify the integrity of these hits.
Bonuses were extremely low.
The risks remain extremely low.
