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Out of shortlisted members, those with highest pair wise alignment score with respect to DDX3X were finally chosen.
The similarity of cochleotopic maps between subjects was tested with a pair wise alignment index (see methods).
Out of these 57 sequences, those with highest pair wise alignment score with DDX3X coding sequence were kept for further study and rest were discarded.
Predicted protein sequences were imported into the ClustalX program [19] and a pair wise alignment was made using the Gonnet 250 score matrix.
Nevertheless, only about 10% of the residues are conserved among the three subunits in the E. coli enzyme, while about 20% of the residues are conserved in each pair wise alignment.
When the sequence identity between a target and its template(s) is above 50%, a pair wise alignment is usually correct and the resulting model quality is comparable to low resolution crystal structures or medium-resolution NMR structures [8].
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The pair-wise alignment approaches will need to align each pair individually thus adding an extra step in network modeling.
We then generated a reverse complement sequence from the entire set, and by aligning each sequence in a pair-wise alignment to HXB2, checked the similarity so that we kept only the forward direction version of the sequence.
In pair-wise alignment, the sequences among the same species had high homology of over 90%.
Likewise, pair-wise alignment between the molecules is constructed using dynamic programming [3], with the compounds being represented as unique SMILES.
Therefore, the MENUET has the advantage over the state-of-the-art study in [17] in that the fullband clustering for mask estimation eliminates the requirement for the additional stage of frequency bin-wise alignment.
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CEO of Professional Science Editing for Scientists @ prosciediting.com