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Parameter values (L, S, and C) used for the search may be altered to obtain fragments of different size or with different levels of conservation (i.e., less conserved for phylogenies of more closely related organisms).
This observation can be interpreted simply as a consequence of different levels of conservation between these regions; R1 is a homologous, conserved region and R3 a variable antigenic region.
For each microRNA, the analysis was performed considering in separated tests the putative target mRNAs with different levels of conservation, according to TargetScan predictions: 'human only' targets, 'conserved' targets and 'highly conserved' targets were evaluated.
The different levels of conservation between these regions lead to a direct application of the syntenic global alignment to the gene prediction problem.
Using a recently developed SVM-based method capable of predicting functionally important cancer mutations [70], [71], we compared the evolutionary conservation distributions of cancer driver mutations and passenger mutations at different levels of conservation (Figure 3B).
These sequences can have very different levels of conservation.
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Since modified amino acids chemically are a distinct type of amino acids, in terms of evolution they might behave differently from their non-modified counterparts (on the top of the different level of conservation).
The proportion of conserved to all possible HCE-gene pairs shows various-degree reduction in the HCE-gene pairs' number under the constraint of different level of conservation (Methods S1, Table S1, Figure S3), the data reflects that using large evolutionary distances would significantly improve the signal to noise ratio.
White and Erickson (2006) showed examples of coiled-coil proteins with different levels of sequence conservation and hypothesized that the conservation depends on the number of interactions along the coiled-coil.
Table 3 compares numbers of autoregulatory feedback loops obtained by counting site predictions Lorg for different levels of sequence conservation with expected numbers calculated based on the introduced probability models.
There are very different levels of evolutionary conservation or orthologous pairing of the GPCR families.
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Justyna Jupowicz-Kozak
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