PMC:1570465 / 38168-39080 JSONTXT

{"target":"https://pubannotation.org/docs/sourcedb/PMC/sourceid/1570465","sourcedb":"PMC","sourceid":"1570465","source_url":"https://www.ncbi.nlm.nih.gov/pmc/1570465","text":"Another widely studied formulation of motif finding is the 'subtle' motifs formulation [17], in which an unknown pattern of a length l is implanted with d modifications into each of the input sequences. The graph version of the problem remains the same except that edges only exist between two vertices that correspond to subsequences whose Hamming distance is at most 2d (since otherwise they cannot both be implanted instances of the same pattern). Edges can either be unweighted, or weighted by the number of mismatches between the corresponding subsequences. Either is easily modeled via slight modification of the ILP given earlier (with variables corresponding to non-existent edges removed, and summations in the edge constraints taken only over existing edges), and the resulting ILP can be used in conjunction with the numerous graph pruning techniques previously developed for this problem (e.g. [17]).","tracks":[{"project":"2_test","denotations":[{"id":"16916460-10977088-1687085","span":{"begin":88,"end":90},"obj":"10977088"},{"id":"16916460-10977088-1687086","span":{"begin":907,"end":909},"obj":"10977088"}],"attributes":[{"subj":"16916460-10977088-1687085","pred":"source","obj":"2_test"},{"subj":"16916460-10977088-1687086","pred":"source","obj":"2_test"}]}],"config":{"attribute types":[{"pred":"source","value type":"selection","values":[{"id":"2_test","color":"#93ecb8","default":true}]}]}}