A universal approach for promoter strength evaluation supported by the web-based tool PromCal

Škrlj, Nives; Vidrih, Zlatko; Dolinar, Marko

doi:10.1016/j.ab.2009.08.033

Cited by 3 publications

(1 citation statement)

References 35 publications

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“…Many experimental methods are available for measuring the promoter activity based on reporter protein activity determination such as luminescence, fluorescence and spectrometry of enzyme products [4]. The main challenge is to fit the data obtained from the wet lab experiments into the computational models.…”

Section: Introductionmentioning

confidence: 99%

A novel sequence and context based method for promoter recognition

Umesh

Dubey

et al. 2014

Bioinformation

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Identification of promoters in DNA sequence using computational techniques is a significant research area because of its direct association in transcription regulation. A wide range of algorithms are available for promoter prediction. Most of them are polymerase dependent and cannot handle eukaryotes and prokaryotes alike. This study proposes a polymerase independent algorithm, which can predict whether a given DNA fragment is a promoter or not, based on the sequence features and statistical elements. This algorithm considers all possible pentamers formed from the nucleotides A, C, G, and T along with CpG islands, TATA box, initiator elements, and downstream promoter elements. The highlight of the algorithm is that it is not polymerase specific and can predict for both eukaryotes and prokaryotes in the same computational manner even though the underlying biological mechanisms of promoter recognition differ greatly. The proposed Method, Promoter Prediction System - PPS-CBM achieved a sensitivity, specificity, and accuracy percentages of 75.08, 83.58 and 79.33 on E. coli data set and 86.67, 88.41 and 87.58 on human data set. We have developed a tool based on PPS-CBM, the proposed algorithm, with which multiple sequences of varying lengths can be tested simultaneously and the result is reported in a comprehensive tabular format. The tool also reports the strength of the prediction.AvailabilityThe tool and source code of PPS-CBM is available at http://keralabs.org

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Section: Introductionmentioning

confidence: 99%

A novel sequence and context based method for promoter recognition

Umesh

Dubey

et al. 2014

Bioinformation

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The ROK like protein of Myxococcus xanthus DK1622 acts as a pleiotropic transcriptional regulator for secondary metabolism

Izzat

Rachid

Ajdidi

et al. 2020

Journal of Biotechnology

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Development of a novel T-vector supporting efficient green-white screening

Bie²,

Zhou

et al. 2013

Biologia

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T-vectors play an important role in cloning of polymerase chain reaction products. In the present study, a novel pUEG-T vector was developed using enhanced green fluorescent protein (EGFP) as an indicator. To improve EGFPbased green-white screening, the lipoprotein mutant promoter, a strong constitutive promoter, was utilized to control the expression of egfp gene. Two other efficient expression elements, the ColE1 replication origin of pUC18 and the expression cassette of pET-28a, were also integrated into pUEG-T vector. Expression analysis demonstrated the efficient accumulation of active EGFPs in Escherichia coli DH5α cells carrying the T-vector precursor pUEG. In T-A cloning using pUEG-T vector, white colonies containing foreign DNA and green colonies having no insertion could be handily distinguished under normal white light, without any chemical inducer or chromogenic substrate. Furthermore, no false positive was observed in any of the tested white colonies. This proves that pUEG-T is an inexpensive, convenient and efficient T-vector.

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A universal approach for promoter strength evaluation supported by the web-based tool PromCal

Cited by 3 publications

References 35 publications

A novel sequence and context based method for promoter recognition

A novel sequence and context based method for promoter recognition

The ROK like protein of Myxococcus xanthus DK1622 acts as a pleiotropic transcriptional regulator for secondary metabolism

Development of a novel T-vector supporting efficient green-white screening

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