Sentence examples for conserved alignment from inspiring English sources
Peptide sequences for each gene were aligned individually with the Muscle software (Edgar 2004); conserved alignment blocks were identified and extracted using Gblocks (Castresana 2000) and concatenated using a custom Perl script.
A second folder named "Rejected – no primers" holds those which contain at least one hot spot region but no conserved alignment blocks suitable for primer development.
We therefore used only conserved alignment blocks, located using Gblocks version 0.91 b [ 72].
Only well-aligned, conserved alignment sites were extracted from each alignment subset using the Gblock program [ 65] with the default option.
All the other alignments which contain at least one "hot spot" region flanked by two conserved alignment blocks are moved in a third folder named "Accepted".
Features of the conserved alignment included N-terminal Somatomedin-B domain(s), inactive pro-cathepsin B-like domains and the signature lipocalin domain.
Because of the e-value threshold in the homology search, poorly conserved alignments are filtered off.
The upstream regions of Tetraodon and Fugu also displayed highly conserved alignments, in particular one, positioned very close to the miRNA, with 88% identity along 126 bp.
These results indicate that the iterative bi-directional mapping strategy is not only useful to identify one-to-one mappings, but also helpful to reveal more functional conserved alignments.
Alignment of homologue protein sequences of different species with ClustalW (http://www.ebi.ac.uk/clustalw/) showed that the serine (position 95), valine (position 140) and asparagine (position 317) residues are highly conserved (alignments, see Supplementary data), supporting that these mutations are most likely pathogenic.
Since NB-LRR loci can comprise up to seven different domain types connected by partially conserved linkers, the RBH approach can result in false positives due to short but highly conserved alignments of highest-scoring sequence pairs (HSPs) in functionally non-relevant (i.e. structural) parts of the protein.
