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Nucleic Acids Research Advance Access published online on May 14, 2009
Nucleic Acids Research, doi:10.1093/nar/gkp379
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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iCODEHOP: a new interactive program for designing COnsensus-DEgenerate Hybrid Oligonucleotide Primers from multiply aligned protein sequences

Richard Boyce1,*, Parmit Chilana2 and Timothy M. Rose3,4,*

1Department of Biomedical Informatics, University of Pittsburgh, UPMC Cancer Pavilion, Suite 301, Pittsburgh, PA 15232, 2Information School, University of Washington, 3Seattle Children's Research Institute and 4Department of Pediatrics, University of Washington, Seattle, WA, USA

*To whom correspondence should be addressed. Tel: +1 206 884 8229; Fax: +1 206 8847311; Email: trose{at}u.washington.edu

Correspondence may also be addressed to Richard Boyce. Tel: +1 412 623 7894; Fax: +1 412 623 2814; Email: rdb20{at}pitt.edu

Received February 2, 2009. Revised April 17, 2009. Accepted April 27, 2009.

PCR amplification using COnsensus DEgenerate Hybrid Oligonucleotide Primers (CODEHOPs) has proven to be highly effective for identifying unknown pathogens and characterizing novel genes. We describe iCODEHOP; a new interactive web application that simplifies the process of designing and selecting CODEHOPs from multiply-aligned protein sequences. iCODEHOP intelligently guides the user through the degenerate primer design process including uploading sequences, creating a multiple alignment, deriving CODEHOPs and calculating their annealing temperatures. The user can quickly scan over an entire set of degenerate primers designed by the program to assess their relative quality and select individual primers for further analysis. The program displays phylogenetic information for input sequences and allows the user to easily design new primers from selected sequence sub-clades. It also allows the user to bias primer design to favor specific clades or sequences using sequence weights. iCODEHOP is freely available to all interested researchers at https://icodehop.cphi.washington.edu/i-codehop-context/Welcome.


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