Document Detail


An efficient algorithm for minimum degeneracy primer selection.
MedLine Citation:
PMID:  17393845     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
Selecting degenerate primers for multiplex polymerase chain reaction (MP-PCR) experiments, called the degenerate primer design problem (DPDP), is an important problem in computational molecular biology and has drawn the attention of numerous researchers in the recent past. Several variants of DPDP were formulated by Linhart and Shamir and proven to be NP-complete. A number of algorithms have been proposed for one such variant, namely, the maximum coverage degenerate primer design problem (MC-DPDP). In this paper, we consider another important variant called the minimum degeneracy degenerate primer design with errors problem (MD-DPDEP), propose an algorithm to design a degenerate primer of minimum degeneracy for a given set of DNA sequences and show experimental results of its performance on random and real biological datasets. Our algorithm combines methodologies in motif discovery and an iterative technique to design the primer.
Authors:
Sudha Balla; Sanguthevar Rajasekaran
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Publication Detail:
Type:  Journal Article; Research Support, U.S. Gov't, Non-P.H.S.    
Journal Detail:
Title:  IEEE transactions on nanobioscience     Volume:  6     ISSN:  1536-1241     ISO Abbreviation:  IEEE Trans Nanobioscience     Publication Date:  2007 Mar 
Date Detail:
Created Date:  2007-03-30     Completed Date:  2007-04-24     Revised Date:  -    
Medline Journal Info:
Nlm Unique ID:  101152869     Medline TA:  IEEE Trans Nanobioscience     Country:  United States    
Other Details:
Languages:  eng     Pagination:  12-7     Citation Subset:  IM    
Affiliation:
Computer Science and Engineering Department, University of Connecticut, Storrs, CT 06269-2155, USA. sub02005@engr.uconn.edu
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MeSH Terms
Descriptor/Qualifier:
Algorithms*
DNA Primers / genetics*
Polymerase Chain Reaction / methods*
Sequence Alignment / methods*
Sequence Analysis, DNA / methods*
Chemical
Reg. No./Substance:
0/DNA Primers

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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