DOMAIN is sensitive at detecting small network alignments that might be deemed by other algorithms to be topologically insignificant.
To simulate different types of alignment errors that might be expected with measurement of IOP in alert chickens, for some calibrations the tonometer was positioned (1) at various distances from the cornea, (2) laterally displaced from the visual axis, or (3) angled away from the visual axis.
Throughout the study described in the paper, we have used a simple global alignment score that might fail to capture a variety of features that represent patterns of conservation such as locally clustered functional regions.
The first stage builds a progressive alignment, the second stage that might be iterated attempts to improve the tree and builds a new progressive alignment according to this tree, and, the third stage performs iterative refinement using a variant of tree-dependent restricted partitioning.
Only by using more samples from different individuals, inter-individual variation that might affect the alignment can be taken into account.
To remove highly similar sequences that might complicate genomic alignments, any annotation with >90% sequence similarity to another annotation was removed from further consideration.
This step was carried out after the check for topological congruence to avoid including incorrect MoLFunCs that might perturb the overall alignment.
At the same, the criterion is not sufficient to suppress all false-positive hits that might originate from chance alignments of TM regions with hydrophobic stretches.
Sequence alignment suggested that TaNAC29 might be located on chromosome 2BS.
Additionally, our parameter setting is rather conservative with the effect that alignments might terminate too early.
From 519 differentially expressed genes, 391 unigenes have significant BLAST hits (75%) and the remaining 25% do not have any significant sequence alignments, which suggests that they might be genes that are novel or have not been reported in any other plant databases.
