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Using a probabilistic approach, we calculate a similarity measure which can be applied to fragments containing only protein sequence, structure or both simultaneously.<\/jats:p><\/jats:sec><jats:sec><jats:title>Results<\/jats:title><jats:p>Proof-of-concept results are given for the different problems. For sequence alignments, the methodology is no better than conventional methods. For structure alignments, the techniques are very fast, reliable and tolerant of a range of alignment parameters. Combined sequence and structure alignments may provide a more reliable alignment for pairs of proteins where pure structural alignments can be misled by repetitive elements or apparent symmetries.<\/jats:p><\/jats:sec><jats:sec><jats:title>Conclusion<\/jats:title><jats:p>The probabilistic framework has an elegance in principle, merging sequence and structure descriptors into a single framework. It has a practical use in fast structural alignments and a potential use in finding those examples where sequence and structural similarities apparently disagree.<\/jats:p><\/jats:sec>","DOI":"10.1186\/1748-7188-3-4","type":"journal-article","created":{"date-parts":[[2012,5,9]],"date-time":"2012-05-09T14:27:24Z","timestamp":1336573644000},"update-policy":"http:\/\/dx.doi.org\/10.1007\/springer_crossmark_policy","source":"Crossref","is-referenced-by-count":9,"title":["Protein sequence and structure alignments within one framework"],"prefix":"10.1186","volume":"3","author":[{"given":"Gundolf","family":"Schenk","sequence":"first","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Thomas","family":"Margraf","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]},{"given":"Andrew E","family":"Torda","sequence":"additional","affiliation":[],"role":[{"role":"author","vocabulary":"crossref"}]}],"member":"297","published-online":{"date-parts":[[2008,4,1]]},"reference":[{"key":"45_CR1","first-page":"345","volume-title":"Atlas of Protein Sequence and Structure","author":"M Dayhoff","year":"1978","unstructured":"Dayhoff M, Schwartz R, Orcutt B: A model of evolutionary change in proteins. 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