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Although it is a reliable tool, CTS is not necessarily an accurate one for measurement of knee alignment when compared to LLR.
A set of genes was identified where the original Genefinder prediction was still being used, where there was little or no transcript evidence to support the CDS and where Jigsaw gave a substantially better alignment when compared to the paralogous genes than the curated CDS.
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The use of structural information by both MAPPIS and CMAPi leads to significantly better alignments when compared to MUSCLE, which uses only sequence information.
The one exception here is the number of variants identified from the CUSHAW3 alignments when compared to other alignments: overall the number of TP SNVs is lower, the number of FP SNVs is higher, and it is the only aligner that produces more than 1,000 FP indels after filtering.
Quantitative results show that CPOL is capable of achieving comparable alignment accuracy when compared to normalized mutual information, while being more robust to imaging artifacts such as noise.
Consequently, these methods obtain lower alignment accuracy when compared to highly accurate geometrical search tools.
This is because some related pathway names do not have very high alignment scores due to the short length of two strings, but the similarities of the two strings can be revealed accurately by the high alignment ratio when compared to other not-so-similar long strings in a single round of search.
These measurements revealed a significant (p < 0.05) increase in mineral nanocrystallite alignment in the LB when compared to the IF region, with increased tissue maturation in wild-type mice; this was absent in mice with rickets.
Manual inspection of selected SIM4 alignments showed apparent sequence inconsistencies, when compared to the secondary alignments [see Additional File 1].
For the remaining datasets of BAliBASE, all consistency-based programs, namely Probcons, T-Coffee, Probalign and MAFFT still produced alignments with higher accuracy when compared to the other five programs.
The aspect of c-axis alignment is of particular interest when compared to a previous study on solution cast caffeine on mica since an alignment of the a-axis was achieved by this preparation route.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com