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Bioinformatics Advance Access published online on February 10, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth075
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received July 30, 2003
Revised October 21, 2003
Accepted October 22, 2003

Article

Poorly-conserved ORFs in the genome of the archaeon Halobacterium sp. NRC-1 correspond to expressed proteins

H. Shmuely 1, E. Dinitz 1, I. Dahan 1, J. Eichler 1*, D. Fischer 2*, B. Shaanan 1*

1 Department of Life Sciences, Ben Gurion University of the Negev, Beersheva 84015, Israel
2 Department of Bioinformatics and Computer Science, Ben Gurion University of the Negev, Beersheva 84015, Israel

* To whom correspondence should be addressed. E-mail: bshaanan{at}bgumail.bgu.ac.il.


  Abstract

Motivation: A large fraction of Open Reading Frames (ORFs) identified as "hypothetical" proteins correspond to either "conserved hypothetical" proteins, representing sequences homologous to ORFs of unknown function from other organisms or to hypothetical proteins lacking any significant sequence similarity to other ORFs in the databases. Elucidating the functions and 3D structures of such orphan ORFs, termed ORFans or PCOs (poorly conserved ORFs), is essential for understanding biodiversity. However, it has been claimed that many ORFans may not encode for expressed proteins.

Results: A genome-wide experimental study of "paralogous PCOs" in the halophilic archaea Halobacterium sp. NRC-1 was conducted. Paralogous PCOs are ORFs with at least one homolog in the same organism, but with no clear homologs in other organisms. The results reveal that mRNA is synthesized for a majority of the Halobacterium sp. NRC-1 paralogous PCO families, including those composed of relatively short proteins, strongly suggesting that these Halobacterium sp. NRC-1 paralogous PCOs correspond to true, expressed proteins. Hence, further computational and experimental studies aimed at characterizing PCOs in this and other organisms are merited. Such efforts could shed light on PCOs' functions and origins, thereby serving to elucidate the vast diversity observed in the genetic material.


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