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Title

DPPrimer A Degenerate PCR Primer Design Tool

 

Authors

Shachi Gahoi1, Arya L1 , Rai Anil2 & Marla SS1*

 

Affiliation

1Department of Computer and Information Sciences, Towson University, Towson, MD 21252, USA; 2Genetic Improvement of Fruits and Vegetables Laboratory, USDA-ARS, Beltsville, MD 20705, USA

 

Email

soma.marla@nbpgr.ernet.in; *Corresponding author

 

Article Type

Software

 

Date

Received March 03, 2013; Revised October 02; Accepted October 19, 2013; Published November 11, 2013

 

Abstract

Designed degenerate primers unlike conventional primers are superior in matching and amplification of large number of genes, from related gene families. DPPrimer tool was designed to predict primers for PCR amplification of homologous gene from related or diverse plant species. The key features of this tool include platform independence and user friendliness in primer design. Embedded features such as search for functional domains, similarity score selection and phylogebetic tree further enhance the user friendliness of DPPrimer tool. Performance of DPPrimer tool was evaluated by successful PCR amplification of ADP-glucose phosphorylase genes from wheat, barley and rice.

 

Availability

DPPrimer is freely accessible at http://202.141.12.147/DGEN_tool/index.html

 

Keywords

Degeneracy, PCR, Primer design.

 

Citation

Gahoi et al.   Bioinformation 9(18): 937-940 (2013)

 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

License

This is an Open Access article which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. This is distributed under the terms of the Creative Commons Attribution License.