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The unbiased alignment process of MSARC may simplify this procedure and improve the reconstruction accuracy, especially in the most problematic cases.
An initial codon-usage unbiased alignment was obtained by extracting the highest-scoring alignment (of possibly multiple alignments) of a TBlastX analysis.
Analysis of the data show a statistically significant correlation between the changes in the exo-metabome of the overexpressing strains and the changes that were predicted based on the unbiased alignment of transcriptomic and exo-metabolomic data.
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HMMSplicer's unbiased approach to alignment, combined with the sequence level power of RNA-Seq, has enormous potential for biological inquiry into alternative splicing.
Because viral consensus can vary substantially between patients it may be difficult to find an existing reference that allows unbiased and complete alignment of reads [ 2, 15].
For TorsinA(E171Q -LULL1(233–470), 808 particles were boxed out and subjected to 'direct classification', an unbiased, reference-free, alignment-free classification function in the PARTICLE software package (www.sbgrid.org/software/title/PARTICLE).org/software/title/PARTICLE
Comparisons of the inferred maximum-likelihood topologies against a concatenation of all gene alignments using the Approximately Unbiased test rejected the null hypothesis of congruent phylogenetic signals for all families (p≤0.01) implying different evolutionary histories among this group of genes.
Individual gene trees were tested for compatibility against the concatenated alignments via the approximately unbiased (AU) test as employed in Consel (Shimodaira 2002).
The thresholds are based on query coverage and alignment identity to allow an unbiased filtering for diverse datasets and databases, in contrast to using unnormalized E-values or alignment scores.
An unbiased estimation of diversity of a population requires the alignment of homologous sequences.
These biases arise because the alignment positions under scrutiny do not constitute an unbiased subsample of the true homologous positions.
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