Independently of the simple motif finder adopted, the output of the first stage is a set of simple motifs with associated position lists of their occurrences, each one ordered by increasing sequence indexes and increasing positions within the sequence.
To detect patterns of protein similarities, we conducted "repertoire-wide" dot-plot analyses using concatamers of var exon1 sequences ordered by isolate and 5' flanking sequence type.
Each set K i is maintained as a vector data structure, each cell of which in turns stores a pointer to a vector containing all occurrences of exactly one m ∈ K i, ordered by increasing input sequence index and increasing position in each sequence.
The levels of evidence and strengths of recommendation for each recommendation are then shown in table 2 and the economic valuation in table 3. The 15 recommendations are ordered by a logical sequence or procedural and chronological hierarchy rather than by any major weight of importance, with the exception of the first two points which constitute the foundation of all subsequent items.
Once this was calculated for each of the 169 ancestral sequences, ancestral sequences were ordered by the number of covered (<5% divergence) extant sequences.
Then, all peptides are ordered by mass range and sequence uniqueness in order to select detectable proteotypic peptides for each protein of interest.
In this section we present and discuss the results of the RNA annotations obtained from the individual tools ordered by their classifications as sequence based homology search tools, structure based homology search tools, and class specific search tools.
The top hits are ordered by their API and sequences with alignment smaller than 95% of query sequence are excluded from ranking.
Thus the collection of parking choice problems parameterized by ( tilde{x} ) amounts to a sequence of efficiency intervals: the sequence is ordered by the lot positions since a larger position induces an efficiency interval with larger values.
Dr. Joseph A. Walder, chief executive of Integrated DNA Technologies, the company that synthesized the polio DNA for Dr. Wimmer, said his company was now considering checking sequences ordered by customers against a database of pathogens.
