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This characteristic requires the use of alignment algorithms that allow for the inclusion of insertions and deletions relative to the reference, and may complicate the detection of structural variation.
The use of alignment of specifically located radioactive capsules may also be applied in other regions to standardize scintigraphic views.
Lately, several qnr genes have been discovered based on sequence homology by use of alignment tools [ 11, 13].
The use of alignment of specifically located point sources may also be applied in other regions to standardize scintigraphic views.
For example, most of the time no justification is provided for the use of alignment methods, typically with default settings followed by subjective manual intervention.
There have also been attempts to infer function from structure without the use of alignment algorithms, such as in enzyme classification [ 20, 21].
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The use of alignment-free methods for comparing sequences has proved useful in different applications.
Thus, use of cross-species conservation data, within an integrative framework significantly (p<0.05, by FET) improved recall rate, and joint use of alignment- and pattern-discovery-based approaches yielded an additional statistically significantly improvement (p<0.05, by FET) over either method in isolation.
A third question is whether to make use of alignments with other species in SEM.
For example, the delineation of OTUs has also been automated via tools that do not make use of alignments or phylogenetic trees (e.g., Greengenes).
The size of current datasets exclude the use of alignment-based techniques.
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