MSA-S-OPT(lambda
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Structure-Informed Multiple Sequence Alignment: A Formal Model and Hardness Results
Announce Type: new Abstract: We formulate a structure-informed multiple sequence alignment problem, denoted MSA-S. The model abstracts biological sequences as strings and structural information as designated position-pairs. It augments a fixed pairwise string score, defined by a fixed non-gap symbol-pair scoring rule and fixed affine gap penalties, with a binary overlap score on designated position-pairs, which can be interpreted as a contact-map overlap score in structural applications....