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Title

Automation of a primer design and evaluation pipeline for subsequent sequencing of the coding regions of all human Refseq genes

 

Authors

Daniel Lai1 & Donald R Love1, 2*

 

Affiliation

1School of Biological Sciences, University of Auckland, Private Bag 92019, Auckland 1142, New Zealand; 2Diagnostic Genetics, LabPlus, Auckland City Hospital, PO Box 110031, Auckland 1148, New Zealand.

 

Email

donald@adhb.govt.nz; *Corresponding author

 

Article Type

Hypothesis

 

Date

Received April 23, 2012; Accepted April 26, 2012; Published April 30, 2012

 

Abstract

Screening for mutations in human disease-causing genes in a molecular diagnostic environment demands simplicity with a view to allowing high throughput approaches. In order to advance these requirements, we have developed and applied a primer design program, termed BatchPD, to achieve the PCR amplification of coding exons of all known human Refseq genes. Primer design, in silico PCR checks and formatted primer information for subsequent web-based interrogation are queried from existing online tools. BatchPD acts as an intermediate to automate queries and results processing and provides exon-specific information that is summarised in a spreadsheet format.

 

Keywords

Primers, Refseq genes, single nucleotide polymorphisms, BatchPD

 

Citation

Lai & Love, Bioinformation 8(8): 365-368 (2012)
 

Edited by

P Kangueane

 

ISSN

0973-2063

 

Publisher

Biomedical Informatics

 

Copyright

Publisher

 

Copyright Transfer Agreement

The authors of published articles in Bioinformation automatically transfer the copyright to the publisher upon formal acceptance. However, the authors reserve right to use the information contained in the article for non commercial purposes.

 

License

This is an open-access article, which permits unrestricted use, distribution, and reproduction in any medium, for non-commercial purposes, provided the original author and source are credited.