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%.
journal_name
Proc Natl Acad Sci U S Aauthors
Alam I,Dress A,Rehmsmeier M,Fuellen Gdoi
10.1073/pnas.0405612101keywords:
subject
Has Abstractpub_date
2004-09-21 00:00:00pages
13814-9issue
38eissn
0027-8424issn
1091-6490pii
0405612101journal_volume
101pub_type
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