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Quantitative sequence-activity models (QSAM)--tools for sequence design.
Department of Organic Chemistry, University of Umeå, Sweden.
Models have been developed that allow the biological activity of a DNA segment to be altered in a desired direction. Partial least squares projections to latent structures (PLS) was used to establish a quantitative model between a numerical description of 68 bp fragments of 25 E.coli promoters and their corresponding quantitative measure of in vivo strength. This quantitative sequence-activity model (QSAM) was used to generate two 68 bp fragments predicted to be more potent promoters than any of those on which the model originally was based. The optimized structures were experimentally verified to be strong promoters in vivo.
PMID: 8441682 [PubMed - indexed for MEDLINE]
PMCID: PMC309176
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Cited by 2 PubMed Central articles
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Engineering proteinase K using machine learning and synthetic genes.
Liao J, Warmuth MK, Govindarajan S, Ness JE, Wang RP, Gustafsson C, Minshull J.
BMC Biotechnol. 2007 Mar 26; 7:16. Epub 2007 Mar 26.
[BMC Biotechnol. 2007]
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ACTIVITY: a database on DNA/RNA sites activity adapted to apply sequence-activity relationships from one system to another.
Ponomarenko JV, Furman DP, Frolov AS, Podkolodny NL, Orlova GV, Ponomarenko MP, Kolchanov NA, Sarai A.
Nucleic Acids Res. 2001 Jan 1; 29(1):284-7.
[Nucleic Acids Res. 2001]