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We showed that divergence patterns in nuclear-encoded tRNA molecules of vertebrate and drosophilid species follow general theoretical predictions for sequence evolution under mutational pressure.
Third, our model allows systematic variation of the phase locking of cells against the theta rhythm, leading to novel predictions for sequence properties, including a dependence of the decoded sequence path length and propagation speed on phase locking.
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Accuracy is measured as the correlation between true and predicted breeding values of last generation individuals in cross-validation and is the average of 50 replicates; *number of SNPs used for prediction; for Sequence, all SNPs are used, for causal SNPs, only 20 or 100 QTN are used.
Our conclusion is that working in single precision does not introduce unacceptable roundoff error for RNA secondary structure prediction for sequences of this size and most likely substantially larger.
We also performed enzyme classification analysis based on Enzyme Commission (EC) numbers predictions for each sequence.
Orthologs, ultraparalogs and subtree-neighboring predictions for each sequence of the tree were generated using the DoRIO procedure.
As output, GreenPhyl generates all the ortholog predictions for each sequence contained in the original multi-fasta file.
By integrating results from different methods, we generate the consensus-based final predictions for local sequence features, three-dimensional structure and function.
To eliminate this redundancy, the gene family which marked the highest score was assigned and the rest of predictions for that sequence were discarded.
This difference can be explained by the differences in the data domain used for the predictions (for example, sequence data, gene expression data, PPIs) and differences in the methods themselves.
The trinity of similar sequence resulting in similarity of structure and function is the cornerstone of the sequence homology concept and the basis for functional predictions for uncharacterized sequences.
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