Sentence examples for many alignments from from inspiring English sources
For a sequence to be classified as Y-linked with the chromosome quotient it must have many alignments from males, and zero or a few alignments from females.
Using the CQ method, a sequence is classified as Y-linked if it has more than 3.33 times as many alignments from male data than from female data, and therefore a CQ less than 0.3.
However, our finding that for so many alignments from cellular life, the best matrix was derived from viral sequences is surprising and the consequence is that ad hoc arguments for choice of matrix may not reasonable.
In addition, this mode of alignment was combined with options that define which and how many alignments should be reported; the option "-k 1 --best" instoucted bowtie to report only the best alignment if more than one valid alignment exists, while the option "-m 1" instructed bowtie to refrain from reporting any alignments for reads having multiple reportable alignments.
Clade model analyses revealed that, after duplication, the selective regime experienced by many alignment sites changed from weak purifying selection to either neutral evolution or weak positive selection.
Using the pairwise data, start and end positions of the modules were estimated from the many alignment regions and were set to cover as much of the sequence as possible, not only the most conserved regions of all the alignments.
Many alignment formats were supported, and feature annotation extracted from SwissProt (Boeckmann et al., 2003) flat-files could be plotted on the alignment to highlight important regions of a sequence.
Many alignment algorithms exist.
There are many alignment formats available.
Many alignment methods often produce reasonable alignments which score worse than alignments with alternative templates.
Many authors use the curated alignments from the Pfam database without parsing for redundancy; this redundancy is more harmful than it seems as it can drastically alter the frequencies of amino acids and the subsequent couplings between them.
