Filling a Protein Scaffold with a Reference.

In mass spectrometry-based de novo protein sequencing, it is hard to complete the sequence of the whole protein. Motivated by this, we study the (one-sided) problem of filling a protein scaffoldS with some missing amino acids, given a sequence of contigs none of which is allowed to be altered, with respect to a complete reference protein P of length n, such that the BLOSUM62 score between P and th...