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The CChMVd LAMP primer sets were designed using the sequences from nonsymptomatic and symptomatic CChMVd isolates in Korea.
We generated position weight matrices using the sequences from the top ten enriched motifs.
An analysis of predicted tropism was performed using the sequences from the plasma virions.
Each potential SNP and insertion/deletion was verified and resolved using the sequences from the cloned PCR product.
There were additional sequence gaps, mostly within scaffolds, in the new assembly that could be patched using the sequences from the Mt3.5 assembly.
We performed a BLASTP search with an E-value below 10-20 againsthehe complete proteome of X. tropicalis by using the sequences from GPCRDB as queries.
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Finally, all consensus sequences were aligned, using the sequence from early 2009 as a reference to detect the mutations as time proceeded.
Again, RT-PCR products were obtained for each sample using the primer pairs of each element and their homology to TvMULEs validated by hybridization using the sequence from the JT strain of T. vaginalis as probe.
For the heterozygous parts of overlapping clones, we used the sequences from P3B2 and P5B8 as the consensus sequence.
We used the sequences from each of the four core histone MUSCLE alignments (H2A, H2B, H3 and H4) as seeds for PSI-BLAST (32) searches.
As this covers only 75% of Pfam version 22, we further used the sequences from 'full dataset' to identify BRPs of 1460 families (16%).
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