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However, current investigation is hampered by the lack of computational methods for systematic evaluating sequence specificity.
The high correspondence between the strengths of the patterns in genome-wide libraries and positioning properties in vitro points to a basic strategy that could be used for development of novel predictive models for identifying nucleosome positions from nucleotide sequence and for evaluating sequence heterogeneity in nucleosome libraries in a meaningful fashion.
RIBOSUM scoring (Bernhart et al., 2008) was added for evaluating sequence similarity.
This composition dependence is important in evaluating sequence conservation across malaria genomes, due to their strong AT bias.
We removed PPI data redundancies by evaluating sequence similarity and then integrated human PPIs with the H-InvDB proteins.
The HCC1187 dataset is a well-recognized baseline dataset from Illumina for evaluating sequence analysis algorithms (Howarth et al., 2011, 2007; Newman et al., 2013).
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The subsequent procedures included summarizing data production, evaluating sequencing quality and depth, calculating length distribution of small RNAs, and filtrating contaminated reads.
The importance of evaluating sequence-related miRNAs during functional analysis has been elegantly exemplified by work on the C. elegans let-7 miRNA family.
Obviously, this is only a very rough way of evaluating sequence-comparison methods, since the resulting tree topologies not only depend on the distance values calculated by the evaluated methods, but also on the tree-reconstruction method that is applied to them.
The raw reads obtained from Solexa sequencing were processed by summarizing data production, evaluating sequencing quality, calculating the length distribution of small RNA reads.
We evaluated sequence polymorphisms of PbP27 gene sequence among isolates, finding some polymorphisms associated with the isolates' phylogenetic origin.
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