Phyre only modelled a small portion of my sequence – why?
By default, Phyre performs a local alignment of your sequence against our fold library. This means if a small portion of your sequence show significant homology to a domain in our library, often only that domain will be modelled. We will instate a global-local mode for Phyre shortly. In the meantime however, if Phyre returns a confident prediction for a subsequence of your sequence, I suggest you cut out that confidently modelled section and resubmit the two remaining portions to see if confident matches can be found for those subsequences.
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