Home

Comprehensive viral oligonucleotide probe design using conserved protein regions

Omar J. Jabado; Yang Liu; Sean Conlan; Phuong-Lan Quan; Hedi Hegyi; Yves Lussier; Thomas Briese; Gustavo F. Palacios; W. Ian Lipkin

Title:
Comprehensive viral oligonucleotide probe design using conserved protein regions
Author(s):
Jabado, Omar J.
Liu, Yang
Conlan, Sean
Quan, Phuong-Lan
Hegyi, Hedi
Lussier, Yves
Briese, Thomas
Palacios, Gustavo F.
Lipkin, W. Ian
Date:
Type:
Articles
Department:
Center for Infection and Immunity
Volume:
36
Permanent URL:
Book/Journal Title:
Nucleic acids research
Abstract:
Oligonucleotide microarrays have been applied to microbial surveillance and discovery where highly multiplexed assays are required to address a wide range of genetic targets. Although printing density continues to increase, the design of comprehensive microbial probe sets remains a daunting challenge, particularly in virology where rapid sequence evolution and database expansion confound static solutions. Here, we present a strategy for probe design based on protein sequences that is responsive to the unique problems posed in virus detection and discovery. The method uses the Protein Families database (Pfam) and motif finding algorithms to identify oligonucleotide probes in conserved amino acid regions and untranslated sequences. In silico testing using an experimentally derived thermodynamic model indicated near complete coverage of the viral sequence database.
Subject(s):
Epidemiology
Virology
Publisher DOI:
http://dx.doi.org/10.1093/nar/gkm1106
Item views:
386
Metadata:
text | xml

In Partnership with the Center for Digital Research and Scholarship at Columbia University Libraries/Information Services | Terms of Use