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Bioinformatics Advance Access published online on October 6, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti706
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© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org
Received July 28, 2005
Revised September 15, 2005
Accepted October 5, 2005

Article

Discovering hidden viral piracy

Eddo Kim 1 and Yossef Kliger 2*

1 Compugen Ltd, Tel Aviv 69512, Israel; Faculty of Life Sciences, Bar-Ilan University, Ramat Gan 52900, Israel
2 Compugen Ltd, Tel Aviv 69512, Israel

* To whom correspondence should be addressed.
Yossef Kliger, E-mail: kliger{at}compugen.co.il


  Abstract

Motivation: Viruses and developers of anti-inflammatory therapies share a common interest in proteins that manipulate the immune response. Large double-stranded DNA viruses acquire host proteins to evade host defense mechanisms. Hence, viral pirated proteins may have a therapeutic potential. Although dozens of viral piracy events have already been identified, we hypothesized that sequence divergence impedes the discovery of many others.

Results: We developed a method to assess the number of viral/human homologs, and discovered that at least 917 highly diverged homologs are hidden in low-similarity alignment hits that are usually ignored. However, these low-similarity homologs are masked by many false alignment hits. We therefore applied a filtering method to increase the proportion of viral/human homologous proteins. The homologous proteins we found may facilitate functional annotation of viral and human proteins. Furthermore, some of these proteins play a key role in immune modulation and are therefore therapeutic protein candidates.


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