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(see Methods for Assignment of Chimeric Junctions).
DSSP and STRIDE use similar methods for assignment based on detecting hydrogen bonds.
> -wrap-foot> Table 2 extends the comparison of SST with other popular methods for assignment on low-resolution structures.
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Dictionary of Protein Secondary Structure (DSSP), a widely used method for assignment of secondary structures has also been integrated in BDE [ 23].
In the Glc residue, H-1 to H-4 and H-6 were assigned using the same method used for assignment of these protons in Glc of saccharide 2. The methine proton, which exhibited correlation peak to H-6 by COSY, was assigned to H-5 (Figure 5 (a)).
What options do you have to decide about the task and the methods for this assignment?
Or as Eric describes it: Interviewer: What options do you have to decide about the task and the methods for this assignment?
Creating an acceptable global alignment above genus level is often impossible for loci with relatively high variation [2], [3], thus limiting the use of this type of methods for species assignment.
Of course it improves the paper to consider alternative methods for module assignment.
Further research will be needed to establish more reliable methods for COD assignment in such cases.
Calculation and evaluation of models were performed with ModPipe software using sequence-sequence, sequence-profile and profile-sequence methods for fold assignment and target-template alignment.
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