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Bioinformatics Advance Access originally published online on March 29, 2005
Bioinformatics 2005 21(11):2580-2589; doi:10.1093/bioinformatics/bti400
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

An algorithm for identification of bacterial selenocysteine insertion sequence elements and selenoprotein genes

Yan Zhang and Vadim N. Gladyshev *

Department of Biochemistry, University of Nebraska Lincoln, NE 68588-0664, USA

*To whom correspondence should be addressed.

Motivation: Incorporation of selenocysteine (Sec) into proteins in response to UGA codons requires a cis-acting RNA structure, Sec insertion sequence (SECIS) element. Whereas SECIS elements in Escherichia coli are well characterized, a bacterial SECIS consensus structure is lacking.

Results: We developed a bacterial SECIS consensus model, the key feature of which is a conserved guanosine in a small apical loop of the properly positioned structure. This consensus was used to build a computational tool, bSECISearch, for detection of bacterial SECIS elements and selenoprotein genes in sequence databases. The program identified 96.5% of known selenoprotein genes in completely sequenced bacterial genomes and predicted several new selenoprotein genes. Further analysis revealed that the size of bacterial selenoproteomes varied from 1 to 11 selenoproteins. Formate dehydrogenase was present in most selenoproteomes, often as the only selenoprotein family, whereas the occurrence of other selenoproteins was limited. The availability of the bacterial SECIS consensus and the tool for identification of these structures should help in correct annotation of selenoprotein genes and characterization of bacterial selenoproteomes.

Availability: The web server interface is freely accessible to users at http://genomics.unl.edu/bSECISearch/

Contact: vgladyshev1{at}unl.edu

Supplementary information: http://genomics.unl.edu/bSECISearch/supplement.html (includes detailed Methods and Figures S1–S3).


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