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Primique: automatic design of specific PCR primers for each sequence in a family
BACKGROUND: In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor out of a family of very similar proteins that is present in a sample, or to des...
Autores principales: | , |
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2007
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045118/ https://www.ncbi.nlm.nih.gov/pubmed/17910777 http://dx.doi.org/10.1186/1471-2105-8-369 |
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author | Fredslund, Jakob Lange, Mette |
author_facet | Fredslund, Jakob Lange, Mette |
author_sort | Fredslund, Jakob |
collection | PubMed |
description | BACKGROUND: In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor out of a family of very similar proteins that is present in a sample, or to design diagnostic assays for the identification of pathogen strains. RESULTS: This paper presents primique, a new graphical, user-friendly, fast, web-based tool which solves the problem: It designs specific primers for each sequence in an uploaded set. Further, a secondary set of sequences not to be amplified by any primer pair may be uploaded. Primers with high sequence similarity to non-target sequences are selected against. Lastly, the suggested primers may be checked against the National Center for Biotechnology Information databases for possible mis-priming. CONCLUSION: Results are presented in interactive tables, and various primer properties are listed and displayed graphically. Any close match alignments can be displayed. Given 30 sequences, the running time of primique is about 20 seconds. primique can be reached via this web address: |
format | Text |
id | pubmed-2045118 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2007 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-20451182007-10-31 Primique: automatic design of specific PCR primers for each sequence in a family Fredslund, Jakob Lange, Mette BMC Bioinformatics Software BACKGROUND: In many contexts, researchers need specific primers for all sequences in a family such that each primer set amplifies only its target sequence and none of the others, e.g. to detect which transcription factor out of a family of very similar proteins that is present in a sample, or to design diagnostic assays for the identification of pathogen strains. RESULTS: This paper presents primique, a new graphical, user-friendly, fast, web-based tool which solves the problem: It designs specific primers for each sequence in an uploaded set. Further, a secondary set of sequences not to be amplified by any primer pair may be uploaded. Primers with high sequence similarity to non-target sequences are selected against. Lastly, the suggested primers may be checked against the National Center for Biotechnology Information databases for possible mis-priming. CONCLUSION: Results are presented in interactive tables, and various primer properties are listed and displayed graphically. Any close match alignments can be displayed. Given 30 sequences, the running time of primique is about 20 seconds. primique can be reached via this web address: BioMed Central 2007-10-03 /pmc/articles/PMC2045118/ /pubmed/17910777 http://dx.doi.org/10.1186/1471-2105-8-369 Text en Copyright © 2007 Fredslund and Lange; 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 | Software Fredslund, Jakob Lange, Mette Primique: automatic design of specific PCR primers for each sequence in a family |
title | Primique: automatic design of specific PCR primers for each sequence in a family |
title_full | Primique: automatic design of specific PCR primers for each sequence in a family |
title_fullStr | Primique: automatic design of specific PCR primers for each sequence in a family |
title_full_unstemmed | Primique: automatic design of specific PCR primers for each sequence in a family |
title_short | Primique: automatic design of specific PCR primers for each sequence in a family |
title_sort | primique: automatic design of specific pcr primers for each sequence in a family |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2045118/ https://www.ncbi.nlm.nih.gov/pubmed/17910777 http://dx.doi.org/10.1186/1471-2105-8-369 |
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