Biology Reference
In-Depth Information
Fig. 5 Effect of option -v, the alignment overhang percentage for similar
sequences. During pairwise alignment, normally every residue of one sequence
is compared to all other residues of the second sequence. Especially for nearly
identical sequences, this is unnecessary since the sequences should align along
the diagonal of the matrix. The -v option represents the percent of residues shifted
past both ends of the longer sequence. Smaller values will cause a narrower swath
requiring fewer cells to be calculated. This will result in quicker alignments but at a
risk of increased mismatches
Fig. 6 Effect of option -V, the alignment overhang percentage for dissimilar
sequences. During pairwise alignment, normally every residue of one sequence
is compared to all other residues of the second sequence. The alignment of more
dissimilar sequences will cause the algorithm to deviate away from the diagonal
of the matrix by a larger number of residues. The -V option represents the
percent of residues shifted past both ends of the longer sequence. Smaller
values will cause a narrower swath requiring fewer cells to be calculated. This
will result in quicker alignments but at a risk of increased mismatches
larger number of residues. This value represents the percent of
residues shifted past both ends of the longer sequence. Smaller
values will result in quicker alignments but at a risk of increased
mismatches. If this option is not specified, the default value is 0.25.
