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In general, these were predicted leaky mutations, where effects (diminished read counts and exon skipping) were inferred against the confounding background of a presumably intact allele.
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Therefore validity can only be inferred against other indicators and across the instruments.
The secondary structures for rrnS and rrnL were inferred by mapping against the appropriate secondary structures for N. americanus [ 32], originally based on Escherichia coli models [ 40] and predicting, either manually or through computer assisted predictions (MFOLD), changes caused by various mutations.
The consensus tree was compared to a reference species tree (Tree of Life) from NCBI, and phylogenies were inferred for orthologous protein sequences against the query sequence.
Functional categories for the core and auxiliary genomes for C. jejuni M1 were inferred through alignments of translated sequences against UniProtKB and the results were summarized in Figure 4.
The liquid holdup in the foam is inferred by calibration against a gamma-ray absorption technique.
To validate this method various sets of source and target proteins from yeast (Saccharomyces cerevisiae) and human (Homo sapiens) are inferred and compared against signaling pathways from KEGG (Kyoto Encyclopedia of Genes and Genomes) [ 20].
The ortholog of Apc5 in C. elegans was not predicted by InParanoid, however could be inferred by a search against nrdb.
A second criticism against cladistic biogeography is that it ignores processes in the biogeographic inference: the area cladogram is inferred without any reference to the underlying biogeographic events.
Gene function was inferred by BLASTP [ 20] searches against the NCBI nr database (as of 6th December , 2012 with an E-value <10-5 cutoff.
Because the observed ratios of non-synonymous (missense) to synonymous (putatively silent) mutations are far smaller than the 3 1 ratio expected from random base substitutions in a genome with close to 25% of each base, strong purifying selection against missense mutations is inferred, rendering such mutations useless for rate estimations.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com