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  Genome-scale design of PCR primers and long oligomers for DNA microarrays

Haas, S. A., Hild, M., Wright, A. P. H., Hain, T., Talibi, D., & Vingron, M. (2003). Genome-scale design of PCR primers and long oligomers for DNA microarrays. Nucleic Acids Research, 31(19), 5576-5581.

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Genre: Zeitschriftenartikel
Alternativer Titel : Nucleic Acids Res.

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 Urheber:
Haas, Stefan A.1, Autor
Hild, Marc, Autor
Wright, Anthony P. H., Autor
Hain, Torsten, Autor
Talibi, Driss, Autor
Vingron, Martin2, Autor           
Affiliations:
1Max Planck Society, ou_persistent13              
2Gene regulation (Martin Vingron), Dept. of Computational Molecular Biology (Head: Martin Vingron), Max Planck Institute for Molecular Genetics, Max Planck Society, ou_1479639              

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 Zusammenfassung: During the last years, the demand for custom-made cDNA chips/arrays as well as whole genome chips is increasing rapidly. The efficient selection of gene-specific primers/oligomers is of the utmost importance for the successful production of such chips. We developed GenomePRIDE, a highly flexible and scalable software for designing primers/oligomers for large-scale projects. The program is able to generate either long oligomers (40–70 bases), or PCR primers for the amplification of gene-specific DNA fragments of user-defined length. Additionally, primers can be designed in-frame in order to facilitate large-scale cloning into expression vectors. Furthermore, GenomePRIDE can be adapted to specific applications such as the generation of genomic amplicon arrays or the design of fragments specific for alternative splice isoforms. We tested the performance of GenomePRIDE on the entire genomes of Listeria monocytogenes (1584 gene-specific PCRs, 48 long oligomers) as well as of eukaryotes such as Schizosaccharomyces pombe (5006 gene-specific PCRs), and Drosophila melanogaster (21 306 gene-specific PCRs). With its computing speed of 1000 primer pairs per hour and a PCR amplification success of 99%, GenomePRIDE represents an extremely cost- and time-effective program.

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Sprache(n): eng - English
 Datum: 2003-10-01
 Publikationsstatus: Erschienen
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 Ort, Verlag, Ausgabe: -
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 Art der Begutachtung: -
 Identifikatoren: eDoc: 173926
ISI: 000185600400019
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Titel: Nucleic Acids Research
  Alternativer Titel : Nucleic Acids Res.
Genre der Quelle: Zeitschrift
 Urheber:
Affiliations:
Ort, Verlag, Ausgabe: -
Seiten: - Band / Heft: 31 (19) Artikelnummer: - Start- / Endseite: 5576 - 5581 Identifikator: ISSN: 0305-1048