Sentence examples for into the alignment from inspiring English sources
This option, called the exclude-fragment or, for short, the xfr option, allows the user to exclude certain pairs of sites, or pairs of segments, from being aligned to each other and, this way, to introduce expert knowledge into the alignment process as well as to explore interactively various alignment alternatives.
The remaining points are then taken as an input into the alignment.
By inserting the electrode-patterned micro-pedestals on the polymer PLC chip into the alignment pits of the silicon optical bench, optical/electrical interconnections were accomplished simultaneously and automatically.
(Side note: Gap penalties are used to prevent ClustalW from inserting an excessive number of gaps into the alignment it produces. The quantities used here are based on many previous studies of protein alignments and are sufficient to achieve this goal).
However, like progressive methods, this technique can be influenced by the order in which the sequences in the query set are integrated into the alignment, especially when the sequences are distantly related.
For example, introduction of staggered gaps into the alignment between BtVsp1 and BtVsp2 better conserves hydrophobic burial properties of a variable loop between helices 2 and 3.
Sequences that did not introduce large gaps (greater than variation observed in previously described proteins) into the alignments were retained for further processing (Additional file 5).
Next, the gap spacing from the template alignment is reintroduced into the pairwise alignment yielding an alignment that may be longer than the template alignment.
Once translated back into nucleotides, the alignment was manually refined.
This software does not take into account the alignment gaps that may lead to underestimated diversity values.
