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Designing multiple degenerate primers via consecutive pairwise alignments

BACKGROUND: Different algorithms have been proposed to solve various versions of degenerate primer design problem. For one of the most general cases, multiple degenerate primer design problem, very few algorithms exist, none of them satisfying the criterion of designing low number of primers that co...

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Detalles Bibliográficos
Autores principales: Najafabadi, Hamed Shateri, Torabi, Noorossadat, Chamankhah, Mahmood
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253518/
https://www.ncbi.nlm.nih.gov/pubmed/18221562
http://dx.doi.org/10.1186/1471-2105-9-55
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author Najafabadi, Hamed Shateri
Torabi, Noorossadat
Chamankhah, Mahmood
author_facet Najafabadi, Hamed Shateri
Torabi, Noorossadat
Chamankhah, Mahmood
author_sort Najafabadi, Hamed Shateri
collection PubMed
description BACKGROUND: Different algorithms have been proposed to solve various versions of degenerate primer design problem. For one of the most general cases, multiple degenerate primer design problem, very few algorithms exist, none of them satisfying the criterion of designing low number of primers that cover high number of sequences. Besides, the present algorithms require high computation capacity and running time. RESULTS: PAMPS, the method presented in this work, usually results in a 30% reduction in the number of degenerate primers required to cover all sequences, compared to the previous algorithms. In addition, PAMPS runs up to 3500 times faster. CONCLUSION: Due to small running time, using PAMPS allows designing degenerate primers for huge numbers of sequences. In addition, it results in fewer primers which reduces the synthesis costs and improves the amplification sensitivity.
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spelling pubmed-22535182008-02-25 Designing multiple degenerate primers via consecutive pairwise alignments Najafabadi, Hamed Shateri Torabi, Noorossadat Chamankhah, Mahmood BMC Bioinformatics Research Article BACKGROUND: Different algorithms have been proposed to solve various versions of degenerate primer design problem. For one of the most general cases, multiple degenerate primer design problem, very few algorithms exist, none of them satisfying the criterion of designing low number of primers that cover high number of sequences. Besides, the present algorithms require high computation capacity and running time. RESULTS: PAMPS, the method presented in this work, usually results in a 30% reduction in the number of degenerate primers required to cover all sequences, compared to the previous algorithms. In addition, PAMPS runs up to 3500 times faster. CONCLUSION: Due to small running time, using PAMPS allows designing degenerate primers for huge numbers of sequences. In addition, it results in fewer primers which reduces the synthesis costs and improves the amplification sensitivity. BioMed Central 2008-01-27 /pmc/articles/PMC2253518/ /pubmed/18221562 http://dx.doi.org/10.1186/1471-2105-9-55 Text en Copyright © 2008 Najafabadi et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Najafabadi, Hamed Shateri
Torabi, Noorossadat
Chamankhah, Mahmood
Designing multiple degenerate primers via consecutive pairwise alignments
title Designing multiple degenerate primers via consecutive pairwise alignments
title_full Designing multiple degenerate primers via consecutive pairwise alignments
title_fullStr Designing multiple degenerate primers via consecutive pairwise alignments
title_full_unstemmed Designing multiple degenerate primers via consecutive pairwise alignments
title_short Designing multiple degenerate primers via consecutive pairwise alignments
title_sort designing multiple degenerate primers via consecutive pairwise alignments
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2253518/
https://www.ncbi.nlm.nih.gov/pubmed/18221562
http://dx.doi.org/10.1186/1471-2105-9-55
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