An analysis of the evolutionary genetic distance of all segmental duplications as a function of the sum of aligned base pairs (43,597 alignments) showed a bipartite distribution, for intrachromosomal and interchromosomal segmental duplications.
Then, where nc(M1) is the non-coding region of M1 and R' is one m-kb long region in nc(M1), and S R, R') is the sum of local alignment scores of all pairs of aligned segments in R and R' output from CHAOS [ 16].
In order to calculate constraint scores for Agrp exons, the STAT sites, and the IREs, we modified the concept of an RS score, such that the score for constraint represents the sum of constrained alignment columns in these regions while ignoring unconstrained alignment columns.
Finally, a Cumulative Alignment Score (CAS) curve is drawn by plotting to each amino acid position of the LGRs the sum of its alignment score to those of all preceding positions.
Orientation was determined by maximizing the sum of the alignment score to this reference, and the elements ordered according to the hit length-weighted average subject position of the homologous regions that were co-orientated with the reference.
Any word in more than one description received the sum of its alignment qualities.
The links were weighted using the sum of the alignment lengths.
COMPASS is a high-performance implementation of the standard sum-of-scores optimal local alignment and its comparison with CORAL implies a lower bound in improvement that can be attributed to the core constraint.
For paired ends, pair scores are computed, each as the sum of the two alignment scores minus a pairing penalty, based on the deviation from the empirical mean insert; and the best scoring pair is reported.
Basically, the optimal N-map of a sequence s over a sequence t is the best way of partitioning the first sequence into N parts and placing them, possibly complementary reversed, over the second sequence in order to maximize the sum of their gapless alignment scores.
