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A new method for RAPD primers selection based on primer bias in nucleotide sequence data

Paper ID Volume ID Publish Year Pages File Format Full-Text
25612 43585 2006 9 PDF Available
Title
A new method for RAPD primers selection based on primer bias in nucleotide sequence data
Abstract

Sequence analysis has proved that decamer nucleotides, used as primers of RAPD (random amplified polymorphic DNA), differ with each other greatly in number of annealing sites in the Arabidopsis thaliana genome. It is called the ‘primer bias’ by the authors. The biased primers produce a highly variable number of amplicons by polymerase chain reaction (PCR). The number of amplicons is proved to correlate with the number of annealing sites. Therefore, a statistical method is proposed for selecting efficient primers based on the primer bias in the genomic sequence. The method was tested by experiment in A. thaliana genome, and the results demonstrate that the method outperforms routine methods and can substantially increase the efficiency of RAPD methodologies. We also proved that the expressed sequence tags (ESTs) show a highly coincident bias pattern with that of the whole genomic sequence, and can therefore be used to assess efficiencies of primers for species whose genomic sequence data are currently unknown.

Keywords
RAPD; Primer bias; Primer selection; Annealing sites
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A new method for RAPD primers selection based on primer bias in nucleotide sequence data
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Publisher
Database: Elsevier - ScienceDirect
Journal: Journal of Biotechnology - Volume 126, Issue 4, 1 December 2006, Pages 415–423
Authors
, , , , , ,
Subjects
Physical Sciences and Engineering Chemical Engineering Bioengineering
Get Full-Text Now
Don't Miss Today's Special Offer
Price was $35.95
You save - $31
Price after discount Only $4.95
100% Money Back Guarantee
Full-text PDF Download
Online Support
Any Questions? feel free to contact us