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Lipase activity is common in staphylococci. Based on the blast of various known staphylococcal lipase DNA sequences, the degenerate primers were derived to amplify a 782-bp consensus lipase gene sequence of Staphylococcus hominis GIMT1.079, which encoded a deduced polypeptide of 260 amino acid (aa) residues. The alignment of aa sequence revealed that this 260-aa partial lipase of S. hominis shared...
Recent development of molecular biological tools has created several research fields such as systems biology, omics studies, and molecular diagnostics. Among them, molecular diagnostics is a new area of clinical diagnosis, and it includes all tests and methods to identify a disease or the predisposition for a disease analyzing DNA, RNA or proteins of an organism. After completion of the human genome...
ZmPP2C was a protein phosphatase 2C gene that we cloned from maize roots. It is an important type of protein phosphatase family. AlignX is a software which can compare homology of many proteins or nucleic acids and search homologous fragments or different bases in high similarity sequences. This paper makes use of the AlignX program to visualize and analyze DNA sequences of ZmPP2C comparing with other...
Polymerase chain reaction (PCR), though invented over twenty years ago and having been developed with much advance, still face challenges nowadays. Long DNA and most high GC content DNA sequences are still hard to amplify. People have had few tools to predict whether a PCR is successful or not before a real PCR experiment is done. In this study, 189 randomly selected short amplicons from human genome...
This paper presents a comparison study between hybridization-ligation method and parallel overlap assembly method as the initial pool generation for solving a Boolean matrix multiplication problem with DNA computing. The focus of this paper is to compare the differences in the working operations for each method, the strategy for designs of DNA sequences and the analysis of the read-out process for...
Ever since Darwin the Tree of Life has provided a framework to study the evolution of organisms. However, comparative genome analyses of microorganisms have shown that genomes are mosaics where different parts have different histories. This is due to horizontal gene transfer that transforms the Tree of Life into a Web of Life where different parts of a genome possess different evolutionary histories...
Gene regulation requires specific protein-DNA interactions. Detecting the short and variable DNA sequences in gene promoter regions to which transcription factors (TF) bind is a difficult challenge in bioinformatics. Here we have developed two-body and three-body interaction potentials that are able to assess protein-DNA interaction and achieve a higher level of specificity in the recognition of TF-binding...
Fixation of advantageous mutations is an important evolutionary force driving the accelerated protein diversification. However, the standard phylogenetic approach to infer positive selection is based on relative rate of nonsynonymous to synonymous substitutions, and requires the knowledge of DNA sequences, hence precludes its application to family of remotely related sequences where saturated substitution...
A novel 2D graphical representation of DNA sequences is introduced in this paper. DNA sequence is coded by assigning pyrimidine-purine to four real number pairs and using the content and position number as parameters. The presented method results in simpler characterizations and comparisons of DNA sequences. It has some important advantages: (A) it avoids loss of position information of A, T, C and...
Nucleotide sequences contain motifs that preserved through evolution because they are important to the structure or function of the molecules. DNA binding site analysis is an important issue in biology experiments as well as in computational methods. To find DNA binding sites that bind to specific transcription factors, we develop a robust mixed effect mixture model (RMEMM). The DNA sequences are...
Nucleotide sequences contain motifs that preserved through evolution because they are important to the structure or function of the molecules. DNA binding site analysis is an important issue in biology experiments as well as in computational methods. To find DNA binding sites that bind to specific transcription factors, we develop a robust mixed effect mixture model (RMEMM). The DNA sequences are...
The integration of genome databases is as one of the complex and challenges to bioinformatics. It is very important to study the complexity of the nature of the data first in the development of any applications. There are several hundred biological databases, analysis tools are available in the online and are freely accessible for the researcher. However, data integration is a difficult task due to...
An anticancer drug dacarbazine (DTIC) was immobilized on a glassy carbon electrode (GCE) by using electrochemical oxidation method. Then the DTIC-modifled GCE was utilized as a stable functional monolayer to further associate with DNA bases and the different blocking effects on the redox reaction of Fe(CN)63- were observed on the different DNA base associated DTIC/GCE, where much bigger blocking...
The regulation of gene transcription in eukaryotes, though not well understood, is known to involve sequence specific recognition and binding of short DNA sequences (transcription elements) by regulatory proteins (transcription factors). The cis acting transcription elements can be found at a considerable distance upstream or downstream from the gene they control and are often orientation independent...
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