Our effort accounts for one category of potential biases between data sets (differences in alignment methodology and data filtering), but other potential concerns should still be recognized.
Genes without COG identifications were assigned to the most probable COG identification and functional description through functional comparison and sequence alignment methodologies [ 19].
The sensitivity of fibroblast guidance on directional cues provided by aligned nanofibers is studied for scaffolds of successively smaller fiber sizes (740 ± 280, 245 ± 85, 140 ± 40, and 80 ± 10 nm) fabricated using mandrel and electrical alignment methodologies for electrospun nanofibers (∼10° angular deviation (AD)), as well as nanoimprint methodologies for perfectly aligned fibers (0° AD).
Yet, in both studies [13, 14], it was shown that the use of reference shapes may provide promise to dramatically improve the throughput of shape-based alignment methodologies.
However, Agrp genomic sequences from distantly related vertebrate species have diverged to the extent that regional conservation is no longer detectable using traditional alignment methodologies [9].
Portions of the nuclear 18S rRNA (18S; 460 or 508 base pairs [bp] depending on alignment methodology, see below) and elongation factor 1 alpha (EF-1α; 345 bp) genes and the mitochondrial cytochrome c oxidase subunit 1 (COI; 381 bp) gene were amplified and sequenced using primers NS1 and NS2a [ 12], EF1For3 and Cho10 [ 56], and L6625 and H7005 [ 57], respectively.
This cannot be controlled and so we chose to measure the LD signals using a micro-volume Couette flow cell apparatus [ 39] as this provides a reproducible alignment methodology to gain more information regarding the orientation of structural elements and chromophores within the amyloid fibrils.
First, the reference sequences within each protein family were aligned using MUSCLE [ 87]; second, the nematode sequences of each family were aligned to their reference sequences using CLUSTALW [ 88], employing the profile alignment methodology [ 89].
The HATS alignment methodology presented here compensates for the effects of resonance variation, thereby increasing the accuracy and interpretability of comparative 2D NMR analyses.
The scaffold alignment methodology is hence highly significant, especially for tissue engineering applications requiring sub-100 nm aligned fibers.
