Comparative homology agreement search: An effective combination of homology-search methods

Alam I, Dress A, Rehmsmeier M, Fuellen G (2004)
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101(38): 13814-13819.

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Abstract
Many methods have been developed to search for homologous members of a protein family in databases, and the reliability of results and conclusions may be compromised if only one method is used, neglecting the others. Here we introduce a general scheme for combining such methods. Based on this scheme, we implemented a tool called comparative homology agreement search (CHASE) that integrates different search strategies to obtain a combined "E value." Our results show that a consensus method integrating distinct strategies easily outperforms any of its component algorithms. More specifically, an evaluation based on the Structural Classification of Proteins database reveals that, on average, a coverage of 47% can be obtained in searches for distantly related homologues (i.e., members of the same superfamily but not the same family, which is a very difficult task), accepting only 10 false positives, whereas the individual methods obtain a coverage of 28-38%.
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Alam I, Dress A, Rehmsmeier M, Fuellen G. Comparative homology agreement search: An effective combination of homology-search methods. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 2004;101(38):13814-13819.
Alam, I., Dress, A., Rehmsmeier, M., & Fuellen, G. (2004). Comparative homology agreement search: An effective combination of homology-search methods. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101(38), 13814-13819.
Alam, I., Dress, A., Rehmsmeier, M., and Fuellen, G. (2004). Comparative homology agreement search: An effective combination of homology-search methods. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101, 13814-13819.
Alam, I., et al., 2004. Comparative homology agreement search: An effective combination of homology-search methods. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 101(38), p 13814-13819.
I. Alam, et al., “Comparative homology agreement search: An effective combination of homology-search methods”, PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, vol. 101, 2004, pp. 13814-13819.
Alam, I., Dress, A., Rehmsmeier, M., Fuellen, G.: Comparative homology agreement search: An effective combination of homology-search methods. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA. 101, 13814-13819 (2004).
Alam, I, Dress, Andreas, Rehmsmeier, Marc, and Fuellen, Georg. “Comparative homology agreement search: An effective combination of homology-search methods”. PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA 101.38 (2004): 13814-13819.
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