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Nucleic Acids Research 2005 33(Database Issue):D178-D182; doi:10.1093/nar/gki060
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Nucleic Acids Research, 2005, Vol. 33, Database issue D178-D182
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved

eBLOCKs: enumerating conserved protein blocks to achieve maximal sensitivity and specificity

Qiaojuan Jane Su, Lin Lu1, Serge Saxonov2,3 and Douglas L. Brutlag2,*

Abgenix, Inc., 6701 Kaiser Drive, MS 11, Fremont, CA 94555, USA, 1 Oracle Corporation, 400 Oracle Parkway, Redwood shores, CA 94065, USA, 2 Department of Biochemistry and 3 Biomedical Informatics, Stanford University, Stanford, CA 94305, USA

* To whom correspondence should be addressed. Tel: +1 650 723 6593; Fax: +1 650 723 6783; Email: brutlag{at}stanford.edu

Received August 16, 2004; Revised and Accepted October 4, 2004

Classifying proteins into families and superfamilies allows identification of functionally important conserved domains. The motifs and scoring matrices derived from such conserved regions provide computational tools that recognize similar patterns in novel sequences, and thus enable the prediction of protein function for genomes. The eBLOCKs database enumerates a cascade of protein blocks with varied conservation levels for each functional domain. A biologically important region is most stringently conserved among a smaller family of highly similar proteins. The same region is often found in a larger group of more remotely related proteins with a reduced stringency. Through enumeration, highly specific signatures can be generated from blocks with more columns and fewer family members, while highly sensitive signatures can be derived from blocks with fewer columns and more members as in a superfamily. By applying PSI-BLAST and a modified K-means clustering algorithm, eBLOCKs automatically groups protein sequences according to different levels of similarity. Multiple sequence alignments are made and trimmed into a series of ungapped blocks. Motifs and position-specific scoring matrices were derived from eBLOCKs and made available for sequence search and annotation. The eBLOCKs database provides a tool for high-throughput genome annotation with maximal specificity and sensitivity. The eBLOCKs database is freely available on the World Wide Web at http://motif.stanford.edu/eblocks/ to all users for online usage. Academic and not-for-profit institutions wishing copies of the program may contact Douglas L. Brutlag (brutlag{at}stanford.edu). Commercial firms wishing copies of the program for internal installation may contact Jacqueline Tay at the Stanford Office of Technology Licensing (jacqueline.tay{at}stanford.edu; http://otl.stanford.edu/).

The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.


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