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This shows that quality of alignment strongly influences the performance of the prediction in the method (M2).
DELTA-BLAST performance, whether it is search sensitivity or quality of alignment, strongly depends on the quality and comprehensiveness of the CDD collection.
There are problems in the above approach, however, because the secondary structures of individual sequences are not exactly the same as the common secondary structure and the quality of the multiple alignment strongly influences the performance of the prediction.
77 RSS (15.4% of all positions) and 158 CSS (31.8% of all positions) were identified along the alignment, strongly suggesting that functional divergence between the CIR sub-families may have occurred according to the criteria generated with protein families of known function [ 36].
The first part of the alignment strongly rejected the tree obtained for the second part (AU test p-value: 4.10-36; SH and KH p-value: 0), and vice versa (AU test p-value: 1.10-06; SH and KH p-value: 0).
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As with D. willistoni, the D. melanogaster SPS1 and SPS2 map to the same location in the A. mellifera genome and analysis of the sequence alignments strongly suggests that the A. mellifera gene is the SPS1 homolog (Figure 4).
Although there's no gene annotated in the cognate region, both human protein similarity and zebrafish EST alignments strongly suggest existence of the C1orf114 gene in this region.
Finally, it is noteworthy that these sequence alignments strongly support the inclusion of Sauroleishmania (of which the taxonomic position remains controversial; reviewed in [ 1]) within Leishmania and perhaps in an intermediary position between both subgenera.
The sequence alignments strongly suggested that the herpesvirus DNA in the oral lesion was HSV-1, although the gorilla-derived amplicon was an outlier in comparison with other HSV-1 isolates (data not shown).
Cunningham's alignment remains strongly literary.
The nuclear sequences corresponding to the 21 first amino acids in the chloroplast clpP1 gene of Spinacia were excluded prior the analysis, because the alignment responded strongly even to small changes in the parameters.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com