However, if the alignments of the flanking regions overlap, combining two local alignments becomes complicated, and an optimal jump from one local alignment to another must be found that is, a gap must be introduced to maximize the alignment score.
This excludes contributions from the other crystalline peaks, putting too much emphasis on the contribution from one alignment of the cellulose crystal lattice.
Thresholds were examined from one male alignment to 50 male alignments.
In such cases, 'shuttling' of one or a few pairs of aligned nucleotides in alignment from one breakpoint to another does not change the overall score.
A major use of interspecies alignments is to transfer functional data from one species to another, making an alignment most useful if aligned functional regions have the same or analogous function in the two species.
UCSC's LiftOver utility allows the conversion of genome coordinates from one species to another, using whole genome alignments (nets and chains) generated by their BLASTZ analysis [ 58, 59].
Minimum spanning distance (smallest number of mutational changes to transition from one sequence to another) was used to classify the alignments into one of five categories (Fig. 3).
