Skip Navigation


Bioinformatics Advance Access originally published online on August 16, 2005
Bioinformatics 2005 21(20):3918-3925; doi:10.1093/bioinformatics/bti633
This Article
Right arrow Full Text Freely available
Right arrow FREE Full Text (Print PDF) Freely available
Right arrow Supplementary Data
Right arrow A correction has been published
Right arrow All Versions of this Article:
21/20/3918    most recent
bti633v1
Right arrow Alert me when this article is cited
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in ISI Web of Science
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrow Search for citing articles in:
ISI Web of Science (8)
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Chavali, S.
Right arrow Articles by Bharadwaj, D.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Chavali, S.
Right arrow Articles by Bharadwaj, D.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oxfordjournals.org

Oligonucleotide properties determination and primer designing: a critical examination of predictions

Sreenivas Chavali 1, Anubha Mahajan 1, Rubina Tabassum 1, Souvik Maiti 2 and Dwaipayan Bharadwaj 1,2,*

1Functional Genomics Unit, Institute of Genomics and Integrative Biology, CSIR Mall Road, Delhi 110 007, India
2Proteomics and Structural Biology Unit, Institute of Genomics and Integrative Biology, CSIR Mall Road, Delhi 110 007, India

*To whom correspondence should be addressed.

Motivation: Precise prediction of melting temperature (Tm), secondary structures and design of oligonucleotides determine the efficiency and success of experimentation in molecular biology. Availability of a plethora of software and the users unawareness about their limitations compromises the accuracy and reliability of the predictions.

Results: Comparative analysis of 56 modules was done for Tm prediction using a large set of oligonucleotide sequences spanning the whole range of GC-content and length. Allawi module of the calculator ‘MELTING’, Nearest Neighbor (NN) of oligo calculator (McLab), NN of Tm Calculation for Oligos (Biomath Calculator, Promega) and HYTHER provided the most precise Tm predictions. A model has also been proposed to calculate the optimum annealing temperature integrating the already reported formulations. Secondary structure predictions of oligonucleotides reveal a large number of structures in contrast to the experimental observations. Of the 11 primer designing tools evaluated, Primer 3 and WebPrimer performed the best for the AT-rich templates, Exon Primer for AT = GC templates, and Primer Design Assistant, Primer3 and Primer Quest for GC-rich templates. This study provides optimal choice for application to the user, increasing the success of a variety of experimentations, especially those that have high-throughput and complex assay designs.

Contact: db{at}igib.res.in

Supplementary Information: The details of the oligonucleotides and of the different modules of Tm prediction considered for the study are provided as Supplementary Information, available at Bioinformatics online.

Received on April 20, 2005; revised on August 14, 2005; accepted on August 15, 2005

Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 Nucleic Acids ResHome page
O. Croce, F. Chevenet, and R. Christen
OligoHeatMap (OHM): an online tool to estimate and display hybridizations of oligonucleotides onto DNA sequences
Nucleic Acids Res., July 1, 2008; 36(suppl_2): W154 - W156.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
R. Andreson, T. Mols, and M. Remm
Predicting failure rate of PCR in large genomes
Nucleic Acids Res., June 1, 2008; 36(11): e66 - e66.
[Abstract] [Full Text] [PDF]

Home page
 BioinformaticsHome page
T. Koressaar and M. Remm
Enhancements and modifications of primer design program Primer3
Bioinformatics, May 15, 2007; 23(10): 1289 - 1291.
[Abstract] [Full Text] [PDF]

Home page
 Nucleic Acids ResHome page
I. Brukner, R. El-Ramahi, I. Gorska-Flipot, M. Krajinovic, and D. Labuda
An in vitro selection scheme for oligonucleotide probes to discriminate between closely related DNA sequences
Nucleic Acids Res., May 14, 2007; 35(9): e66 - e66.
[Abstract] [Full Text] [PDF]


Disclaimer:
Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.