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. 2014 Jul 25;15(1):252. doi: 10.1186/1471-2105-15-252

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© Deng and Cheng; licensee BioMed Central Ltd. 2014

This article is published under license to BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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Tracing back from the AS matrix by integrating the evolutionary coupling information. In query q, the coupled position of i is k _q(i)_, and that of i-1 is k _q(i − 1). In template t, the coupled position of j is k _t(j)_, and that of j-1 is k _t(j − 1). M _q(i) is the corresponding position in template t matched to position i in q during the original tracing-back. M _t(j) is the corresponding position in query q matched to position j in t during the original tracing-back. Additional EC scores are added into the corresponding elements in the AS matrix as shown in the figure so that the correct tracing back is performed.