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Smaller sets of diverse sequences for PI3Ks (classes I, II, and III) were also collected and trimmed to begin at the helical domain.
Summarizing, the capability of antaRNA to reliably produce highly diverse sequences for a given structure, coupled with the precise GC targeting, will help to explore the sequence space for RNA design problems.
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For the generation of phylogenetic trees, the most diverse sequences of each subgroup were aligned with ClustalW [ 18].
However, replacing missing residues with XXs does not work with large numbers of MVP sequences, or for more diverse sequences such as for invertebrates, as there are gaps in the ASR due to sequence divergence, rather than there being a single sequence region missing.
A collection of ten clade C envelope genes with diverse sequences was assembled for this study.
The general conservation of the histidine in Cmr4 is strong (100% for our set of 30 selected diverse sequences), and the same holds for the Csm4 and Csb3 families; in other families (e.g. Cmr6) the conservation is less pronounced but still traceable in at least 50% of the sequences (see the consensus shown in the Additional File 1 ).
Thus, using more diverse peptides might be required to predict binding energy for more diverse sequences.
Most of these clans are known for short and diverse sequences.
The unannotated small RNAs comprised a large number of diverse sequences with low expression and accounted for 38.91% of the unique small RNAs and 9.00% of the total small RNAs.
Even within the REase family the HNH enzymes exhibit diverse sequence specificity: TTA↑AT↓TAA for PacI, ↑CGWCG↓ for Hpy99I, G↑GTAC↓C for KpnI and CAC↑NNN↓GTG for DraIII.
For this purpose, we assembled a collection of ten clade C envelope genes with diverse sequences.
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