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In contrast to the benign conditions, no statistically significant correlations with sequence divergence were observed for any stress, irrespective of whether they were calculated for domesticated or wild strains (not shown).
For the BP ontology, the normalization strategy using the GO-universal idea (Nunivers strategy) outperforms other normalization techniques by consistently showing one of the highest correlations with sequence, Pfam and EC similarity, except for resolution, where the strategy of using the highest IC value (Nmax strategy) performs better.
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No positive relationship could be revealed for ipsilateral M1 and either force differences or sequence learning (r <−0.222, p>0.186, Figure 7B for correlation with sequence learning).
The information coefficient idea consistently outperforms the relevance approach, showing highest correlation with sequence, Pfam, and EC similarity, as well as for resolution.
The fact that no significant correlation with sequence length can be observed for RCA values on artificial gene sequences provides further support to the hypothesis of selection for translational efficiency in long gene sequences.
We then counted the number of species in which the 5′ free energy has a negative Spearman rank correlation with sequence length and also the number of species in which the correlations are significant.
Looking at different Pearson's correlations for the topology-based approaches, the GO-universal approach shows the highest correlation with sequence and Pfam similarity for the BP ontology, while Zhang et al. is highest for EC similarity.
The correlation with sequence conservation was generally weak: The ubiquitin module formed from the DD dataset and the rRNA processing modules in the ER and CC were the most correlated with k.in.in
An average recombination rate was also estimated along the genome over the four pedigrees and was used to carry out further analyses in relation to correlation with sequence features.
At first, we removed singletons shorter than 200 bp because the percentage of BLAST hits usually shows positive correlation with sequence length, as has been confirmed previously in sweet potato [ 41] and celery [ 42].
Their correlation with sequences of the loess series is poorly documented due to the lack of reliable fossil and stratigraphic evidence.
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