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This means that we are not interested in alignments where the corresponding splicing sites (one from each sequence) do not align exactly.
For BLAST, to know this is a chimeric read we would need to ask it to report all the alignments of the 400 bp repeat, which is costly and wasteful because in general we are not interested in alignments of short repetitive sequences contained in a longer unique sequence.
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Moreover, we are only interested in the alignments that include the seed, since the other alignments are locatable through the conventional methods using the original query sequence.
We are typically more interested in the best alignment or best few alignments, covering each region of the query sequence.
At the outset of the War of 1812, the Americans were interested in assessing the alignment of the native tribes in regards to their loyalty to Britain.
Apart from the analysis of the convergence to a common language in the case of a fully autonomous robot team without human intervention we are also particularly interested in analyzing how the syntactic alignment of the robot team can be influenced or mediated by humans.
Be interested in their interests.
Out of the four alignment programs we are interested in, Novoalign adopts a hash table algorithm, while SOAP2, Bowtie, and BWA adopt the FM-index (Table 1).
We identify duplications during pairwise alignment, and so we are interested in generating multi-genome anchors that contain only a single segment per genome.
We were therefore interested in understanding how these atoms contributed to different longitudinal shifts of the structures in the alignments.
The features one is interested in and the way in which these features are described ultimately define the correct alignment, and in theory, given a set of sequences, each feature type may define a distinct optimal alignment.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com