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By doing so, a strong filter was created to select against "false" SNPs resulting from alignment of highly homologous duplicated sequences as opposed to genuine SNPs derived from single-copy sequences in the sequenced genome fraction (Fig. 2).
We employed CuffDiff [ 48] to determine gene expression using SAM files resulting from alignment, annotated gene file upper quantile normalization and masking of rRNA sequences.
Previous characterizations of allelic ratios using RNA-Seq are subject to a number of caveats, most notably high read depth requirements [ 29- 31] and underrepresentation of variant versus reference alleles [ 32, 33] resulting from alignment algorithms penalizing variant alleles as mismatching errors when compared to the reference genome.
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The partial sequence resulted from alignment and assembly of the ESTs of this cluster was used to obtain the full length of the Sra-til.
Thus, our results confirm previous findings [19] that topological variation may result from alignment uncertainty and extend this conclusion to the case of uncertainty in the specification of an evolutionary model.
Note that the variability around the mean values may result from alignment errors from the subtomogram averaging.
One may suspect that this observation has resulted from alignment errors, leading to increased dN and dN/ dS ratios in longer exons.
The distribution of the calculated Ka/Ks ratios for the contigs was found to be ranging from 0.0132 to 6.4000; however any Ka/Ks value greater than 2.5000 was discarded during the analysis assuming that such high values likely resulted from alignment errors.
Alignment artifacts, resulting from incorrect alignments of the RNA-seq reads to the genome, have a great potential of negatively impacting our identification of SSS events.
Foliation, planar arrangement of structural or textural features in any rock type, but particularly that resulting from the alignment of constituent mineral grains of a metamorphic rock of the regional variety along straight or wavy planes.
For this, conserved regions resulting from the alignment of 26 published partial sequences of such gene were used.
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