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Contending qualifications are often made needlessly exclusive, as N.B.A. fans and the media have been trained to look for a particular alignment of superstars or attempt to fit potential contenders into a specific mold.
The P -value for a particular alignment a is estimated as where is the total number of possible contig pairs, x is the assembly number and n is the total number of assemblies.
For a particular alignment a a P -value is calculated as, where is the fraction of non-aligned overhang and l a O is the number of nucleotides that have to be clipped if the two contigs would be merged.
The algorithm does not require the adjustment or modification of the alignment scoring scheme(s) that is usually tuned for a particular alignment purpose, e.g. cross-species, contig or read alignments.
While there is no clear trend between the number of unique distances and the number of TC score differences for a particular alignment program, this trend can be seen across the different programs Mafft shows the fewest number of differences in TC scores and Kalign the most.
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Structural alignment is the most critical step in CoMFA study and the resulting model is often sensitive to a particular alignment.
As it is not possible to prefer one particular alignment over another, we believe this is a better option than randomly choosing a particular alignment of the contig.
Automated operation provides the added benefit of reduced energy consumption by employing consistent acceleration, cruising and braking parameters optimized for the particular alignment and train technology.
Alignments were then submitted to ProtTest version 1.2.6 [ 100] to determine the best-fit model protein substitution for each particular alignment.
The Fhom Estimator helps determine a specific E-Value cutoff for a particular set of alignment hits, above which the number of homologs is negligible.
The likelihood of a tree for a particular site in an alignment is the probability of that site pattern, given the tree (both topology and edge weights) and a substitution model.
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