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Dual-genome primer design for construction of DNA microarrays
KTH, Skolan för bioteknologi (BIO).ORCID-id: 0000-0002-3627-6899
Department of Molecular Evolution, Evolutionary Biology Center, Uppsala University.
KTH, Skolan för bioteknologi (BIO).ORCID-id: 0000-0002-4657-8532
2005 (engelsk)Inngår i: Bioinformatics, ISSN 1367-4803, E-ISSN 1367-4811, Vol. 21, nr 3, s. 325-332Artikkel i tidsskrift (Fagfellevurdert) Published
Abstract [en]

Motivation: Microarray experiments using probes covering a whole transcriptome are expensive to initiate, and a major part of the costs derives from synthesizing gene-specific PCR primers or hybridization probes. The high costs may force researchers to limit their studies to a single organism, although comparing gene expression in different species would yield valuable information. Results: We have developed a method, implemented in the software DualPrime, that reduces the number of primers required to amplify the genes of two different genomes. The software identifies regions of high sequence similarity, and from these regions selects PCR primers shared between the genomes, such that either one or, preferentially, both primers in a given PCR can be used for amplification from both genomes. To assure high microarray probe specificity, the software selects primer pairs that generate products of low sequence similarity to other genes within the same genome. We used the software to design PCR primers for 2182 and 1960 genes from the hyperthermophilic archaea Sulfolobus solfataricus and Sulfolobus acidocaldarius, respectively. Primer pairs were shared among 705 pairs of genes, and single primers were shared among 1184 pairs of genes, resulting in a saving of 31% compared to using only unique primers. We also present an alternative primer design method, in which each gene shares primers with two different genes of the other genome, enabling further savings.

sted, utgiver, år, opplag, sider
2005. Vol. 21, nr 3, s. 325-332
Emneord [en]
sulfolobus-solfataricus, gene, coexpression, initiation
HSV kategori
Identifikatorer
URN: urn:nbn:se:kth:diva-14479DOI: 10.1093/bioinformatics/bti001ISI: 000226605700007Scopus ID: 2-s2.0-13844264518OAI: oai:DiVA.org:kth-14479DiVA, id: diva2:332520
Merknad
QC 20100830Tilgjengelig fra: 2010-08-05 Laget: 2010-08-05 Sist oppdatert: 2017-12-12bibliografisk kontrollert
Inngår i avhandling
1. Microarray-based investigation of genome and transcriptome organisation in the archaeon sulfolobus
Åpne denne publikasjonen i ny fane eller vindu >>Microarray-based investigation of genome and transcriptome organisation in the archaeon sulfolobus
2005 (engelsk)Doktoravhandling, med artikler (Annet vitenskapelig)
sted, utgiver, år, opplag, sider
Stockholm: KTH, 2005. s. 47
Emneord
Biotechnology, microarray, Sulfolobus, gene expression, archaea, mRNA decay, genome evolution, Bioteknik
HSV kategori
Identifikatorer
urn:nbn:se:kth:diva-142 (URN)91-7283-979-1 (ISBN)
Disputas
2005-03-11, Sal D1, Lindstedtsvägen 17, Stockholm, 10:00
Opponent
Veileder
Merknad
QC 20100830Tilgjengelig fra: 2005-03-03 Laget: 2005-03-03 Sist oppdatert: 2010-08-30bibliografisk kontrollert

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