In the first step of the string-based database search, mtDNA profiles whose sequence ranges cover that of the query profile are converted into strings and shortened to represent the ranges of the query profile, if necessary.
It also explores the utility of the information by explaining the range of query options available, from using interactive web displays, to online data mining tools and connecting directly to the data servers programmatically.
These mechanisms index on both the start and end positions at the same time meaning that we can rapidly interrogate the index to identify sequences visible within a given range, typically in O(R* log(N)) complexity, where N is the length of the contig and R is the size of the query range.
If at least one of the hits fulfils the limit given by the "filter threshold", the hit that is longer and has higher identity to the reference within a range of same query positions is kept.
BLAST E-values in both forward and reverse direction ranged between 10−27 and 10−32, with sequence identities ranging from 45% to 52% across 66% to 74% of the query sequence for AtNRT3.1 and ≈41% across ≈85% of the query sequence for AtNRT3.2CT (Graphical representation of the dicot – monocot RBH analysis can be seen in Figure S1).
The range of databases queried by similarity search and the tracking of homology beyond a single 'best' hit maximizes the opportunity to obtain this annotation.
In the immediate future, we hope to expand the range of querying possible from the IKMC BioMart portal by including two new datasets currently being developed by members of the I-DCC.
Once established, the database routine can seamlessly extend the range of data queries to include statistics based on a broader genomic region, rather than a single base-pair location.
The prediction of absolute ligand-receptor binding affinities is essential in a wide range of biophysical queries, from the study of protein-protein interactions to structure-based drug design.
A number of other filters performed within close range of the Boynton et al. precision query (1.6-2.0 1.6-2.0the health-evidence.ca SR search filter having slightly less precision at 1.4.
