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Exact(2)
In contrast to conventional exhaustive grid search, this method can be treated as a deterministic analog of random search.
In addition to the intron retention search, this method was repeated for partial intron retention where an exon was extended to include the STEP.
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Besides the pre-computation expense to determine the reference shapes to use and to generate the 3-D fingerprint for all conformers to be searched, this method has an important drawback.
Since this case involves only present people, all the problems discussed above will reappear in the search of this method.
A new approach based on a single-reference-station mode has been published by Kim and Langley (2007) that nullifies the effect of the differential ionosphere in an ambiguity search process; this method provides a number of interesting results.
Diamonds reflect 85% of the light that hits them, so they will be very shiny when found! Surface searching: If you don't have a lot of time to spend at the Park or need an easy way to search, try this method.
On the other hand, the INFERNAL software applies to more general searches using alignments of both sequences and structures of seed RNAs; however successful searches using this method largely depend on the prerequisite that the candidate RNA is highly conserved at both sequence and structural levels with the seed RNAs used for the search.
For a complex problem with huge searching space, this method may encounter difficulty in finding the optimal solution and risk of divergence.
Iteratively, we searched with this method as long as we were able to find new snoRNA homologs.
In conclusion, the sensitivity of the HMM searches makes this method more successful than BLAST to identify ISs on metagenomic samples, generating less false positives and providing a better picture of the IS diversity.
The 'structure search' option was used; this method searches iMembrane's database for homologous structures using pairwise structure alignment.
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