scholarly journals Rule-Based Knowledge Acquisition Method for Promoter Prediction in Human andDrosophilaSpecies

2014 ◽  
Vol 2014 ◽  
pp. 1-14 ◽  
Author(s):  
Wen-Lin Huang ◽  
Chun-Wei Tung ◽  
Chyn Liaw ◽  
Hui-Ling Huang ◽  
Shinn-Ying Ho

The rapid and reliable identification of promoter regions is important when the number of genomes to be sequenced is increasing very speedily. Various methods have been developed but few methods investigate the effectiveness of sequence-based features in promoter prediction. This study proposes a knowledge acquisition method (named PromHD) based on if-then rules for promoter prediction in human andDrosophilaspecies. PromHD utilizes an effective feature-mining algorithm and a reference feature set of 167 DNA sequence descriptors (DNASDs), comprising three descriptors of physicochemical properties (absorption maxima, molecular weight, and molar absorption coefficient), 128 top-ranked descriptors of 4-mer motifs, and 36 global sequence descriptors. PromHD identifies two feature subsets with 99 and 74 DNASDs and yields test accuracies of 96.4% and 97.5% in human andDrosophilaspecies, respectively. Based on the 99- and 74-dimensional feature vectors, PromHD generates several if-then rules by using the decision tree mechanism for promoter prediction. The top-ranked informative rules with high certainty grades reveal that the global sequence descriptor, the length of nucleotide A at the first position of the sequence, and two physicochemical properties, absorption maxima and molecular weight, are effective in distinguishing promoters from non-promoters in human andDrosophilaspecies, respectively.

Molecules ◽  
2019 ◽  
Vol 24 (6) ◽  
pp. 1049 ◽  
Author(s):  
Rosalía Rodríguez-Dorado ◽  
Clara López-Iglesias ◽  
Carlos García-González ◽  
Giulia Auriemma ◽  
Rita Aquino ◽  
...  

Processing and shaping of dried gels are of interest in several fields like alginate aerogel beads used as highly porous and nanostructured particles in biomedical applications. The physicochemical properties of the alginate source, the solvent used in the gelation solution and the gel drying method are key parameters influencing the characteristics of the resulting dried gels. In this work, dried gel beads in the form of xerogels, cryogels or aerogels were prepared from alginates of different molecular weights (120 and 180 kDa) and concentrations (1.25, 1.50, 2.0 and 2.25% (w/v)) using different gelation conditions (aqueous and ethanolic CaCl2 solutions) and drying methods (supercritical drying, freeze-drying and oven drying) to obtain particles with a broad range of physicochemical and textural properties. The stability of physicochemical properties of alginate aerogels under storage conditions of 25 °C and 65% relative humidity (ICH-climatic zone II) during 1 and 3 months was studied. Results showed significant effects of the studied processing parameters on the resulting alginate dried gel properties. Stability studies showed small variations in aerogels weight and specific surface area after 3 months of storage, especially, in the case of aerogels produced with medium molecular weight alginate.


Author(s):  
Darya Plinere ◽  
Arkady Borisov

SWRL: Rule Acquisition Using Ontology Nowadays rule-based systems are very common. The use of ontology-based systems is becoming ever more popular, especially in addition to the rule-based one. The most widely used ontology development platform is Protégé. Protégé provides a knowledge acquisition tool, but still the main issue of the ontology-based rule system is rule acquisition. This paper presents an approach to using SWRL rules Tab, a plug-in to Protégé, for rule acquisition. SWRL rules Tab transforms conjunctive rules to Jess rules in IF…THEN form.


Author(s):  
Qing-Hua Zhang ◽  
Long-Yang Yao ◽  
Guan-Sheng Zhang ◽  
Yu-Ke Xin

In this paper, a new incremental knowledge acquisition method is proposed based on rough set theory, decision tree and granular computing. In order to effectively process dynamic data, describing the data by rough set theory, computing equivalence classes and calculating positive region with hash algorithm are analyzed respectively at first. Then, attribute reduction, value reduction and the extraction of rule set by hash algorithm are completed efficiently. Finally, for each new additional data, the incremental knowledge acquisition method is proposed and used to update the original rules. Both algorithm analysis and experiments show that for processing the dynamic information systems, compared with the traditional algorithms and the incremental knowledge acquisition algorithms based on granular computing, the time complexity of the proposed algorithm is lower due to the efficiency of hash algorithm and also this algorithm is more effective when it is used to deal with the huge data sets.


1971 ◽  
Vol 49 (9) ◽  
pp. 999-1004 ◽  
Author(s):  
M. C. Shaw ◽  
T. Viswanatha

The physicochemical properties of chymotrypsin-P obtained by the papain activation of chymotrypsinogen have been investigated. The molecular weight of this enzyme as determined by gel filtration technique has been found to be 24 000 ± 1000. The amino acid residues occupying the N-terminal positions and the composition of the B- and C-chains of chymotrypsin-P are identical with those found in α-chymotrypsin. Thus the difference between the two enzymes is restricted to the composition of their A-chains.


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