This segment-based multiple alignment program is known to produce better alignments for the purpose of phylogenetic footprinting than does the tree-based global multiple alignment program ClustalW [ 43], because it starts by identifying short conserved regions and then incorporates them into a multiple alignment [ 44].
With the existence of reference alignments specifically compiled for the purpose of RNA alignment benchmarks, program parameters can be specifically optimized for RNA alignments.
We truncated the gaps to shorten the alignment to 252 residues for the purpose of analysis.
On aligning a sequence with itself for the purpose of identifying repeat patterns, the sub-optimal alignments become obscured by the best (and most obvious) alignment.
A maximum of two mismatches was permitted for the purpose of alignment.
The table 2 of the Pei et al. study showed the diversities of the 16S rRNA genes after masking (for the purpose of alignment) and the diversities of the masked hypervariable regions, whereas our study showed the diversities of full-length 16S rRNA genes for the purpose of HGT study.
The position of each printhead can be independently controlled for the purpose of printhead alignment, by which print quality is improved without tightening the manufacturing tolerances.
For the first time, we have proposed to use the NH2-functionalized polymer film for the alignment and the immobilization of DNA molecules for the purpose of applying them to nanodevices.
A reference database comprising a unique set of RAD loci was created for the purpose of sequence alignment and identification of polymorphisms across individuals.
For the purpose of visualization, alignment columns were colored using Jalview [ 23], with the ClustalX coloring conventions [ 24] and conservation color increment set at 10. Profile-against-profile searches were performed using the HHPred method [ 25].
Due to the different sequencing technology used in the present study, our reference transcriptome has fewer long contigs but a significantly higher number of total contigs and contigs with alignments (Table 1), which is more relevant for the purpose of detecting differentially expressed genes.
