The FRPC wire tested in this study has been designed and manufactured with the intention to function as wire used in the initial alignment phase of orthodontic treatment with high esthetic value.
Currently, ClinSeK only realigns indels that are found in the initial alignment.
In the initial alignment and annotation, some small RNA tags were mapped to more than one category.
Excel file containing the position of excluded regions in the initial alignment and characteristics of each nuclear and plastid data matrix.
Before the second alignment, the customized reference was updated to ensure that one allele was present at each heterozygous site predicted in the initial alignment, and non-reference alleles were added to the separate variant file.
For each candidate TSR, we estimated its relative abundance by recording the number of reads that covered the junction position in the initial alignment, and reads with insertion or deletions were excluded.
This has been shown to produce superior results as well as being able to correct errors in the initial alignment between target sequence and template structures (Burke et al., 1999).
The adjustments in the initial alignment were: TM4: The sequence LLTKN in adrb2 was moved to fill a gap at the N terminus of TM4, and the sequence C4.58PLLF in drd2 was moved to fill a gap between Ser4.57 and Cys4.58.
If there are base mismatches or indels in the initial alignment of this overlap region to either reference location, then each reference alignment is trimmed back until it consists of only perfect matches to the reference genome in the overlap region.
The draft genomes were included in the initial alignment to provide better representation of the strains across the species; however, we did not include sequences from these genomes in our sets of positional homologs as annotation of these genomes was incomplete and we wanted to only include annotated protein-coding genes.
