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Search Results: 1 - 10 of 694 matches for " bioinformatics "
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A novel bioinformatic approach for Staphylococcal Vaccine development
M. R. Pourmand,S. Foster
Tehran University Medical Journal , 2006,
Abstract: Background: Staphylococcus aureus and Staphylococcus epidermidis are major human pathogens of increasing importance due to the spread of antibiotic resistance. Novel potential targets for therapeutic antibodies are products of staphylococcal genes expressed during human infection. Previously, the secreted and surface-exposed proteins among seroreactive antigens have been discovered. Furthermore, approximately 60 immunogenic proteins were identified and have shown that bacterial surface display is uniquely suited to assess the value of the antigenic epitope. Methods: Using a bioinformatic analysis, a novel gene family was identified in Staphylococcus aureus and S. epidermidis. NCBI (National Center for Biotechnology Information) BLAST and TIGR search were used for identification of the loci on Staphylococcal genomes. Results: The members of nine gene family from S. aureus based on a conserved C-terminal domain following an N-terminal domain which varies in sequence and length. Further Blast P searches for paralogues revealed the novel Sca gene family in S. epidermidis has also highly conserved 110 amino acid C-terminal domain. Thus the Sca family has a conserved domain across different genera. Conclusion: Further studies to determine the role of the conserved Sca domain in ligand binding and demonstration of conserved epitope may establish the domain as a credible target for cross species vaccination.
A Genetic Optimization approach for finding common Motif in Biological Sequences
Vishal,Shailendra Singh
International Journal of Computer Technology and Applications , 2011,
Abstract: The field of Bioinformatics is gaining much attention these days due to advancement of computer programs and molecular biology, but there are many human activities which are lying unknown yet. Finding common motif is also a major topic in the field. As with the similarity in the sequences, their families and activities can be identified easily when one of the sequences is tested. The common motif finding can help finding unknown members of a family and can help in applications like drug design. In this paper, it is proposed to find common motif in biological sequences. Here RNA sequences are used. The paper is divided mainly in to three sections. Firstly some basics of bioinformatics are discussed followed by the proposed approach and finally the result and conclusions are presented.
Prot-Class: A bioinformatics tool for protein classification based on amino acid signatures  [PDF]
Jens Lichtenberg, Brian D. Keppler, Thomas Conley, Dazhang Gu, Paul Burns, Lonnie R. Welch, Allan M. Showalter
Natural Science (NS) , 2012, DOI: 10.4236/ns.2012.412A141

Knowledge about characteristics shared across known members of a protein family enables their identification within the complete set of proteins in an organism. Shared features are usually expressed through motifs, which can incorporate specific patterns and even amino acid (AA) biases. Based on a set of classification patterns and biases it can be determined which additional proteins may belong to a specific family and share its functionality. A bioinformatics tool (Prot-Class) was implemented to examine protein sequences and characterize them based upon user-defined AA composition percentages and user defined AA patterns. In addition the tool allows for the identification of repeated AA patterns, biased AA compositions within windows of user-defined length, and the characteristics of putative signal peptides and glycosylphosphatidylinositol (GPI) lipid anchors. ProtClass is general purpose and can be applied to analyze protein sequences from any organism. The Prot-Class source code is available through the GNU General Public License v3 and can be accessed via the Google Code Repository: http://code.google.com/p/prot-class/.

Development of an Algorithm for Reconstructing a Comprehensive Pathway Model: Application to Saccharomyces cerevisiae  [PDF]
Itaru Takeda, Masayuki Machida, Sachiyo Aburatani
Journal of Biomedical Science and Engineering (JBiSE) , 2015, DOI: 10.4236/jbise.2015.88047
Abstract: The generation of bioactive products by microbial bioprocesses is important for drug discovery, functional food development, and other beneficial purposes. Many pathways contribute to the production of these bioactive compounds, but important knowledge for improving productivity still remains in hidden pathways. Recently, an abundance of knowledge about metabolic pathways has been accumulated in metabolic pathway databases, such as BioCyc and KEGG. Many by-products are chemically transformed and actually used in other enzymatic reactions. In this work, we developed an algorithm for the reconstruction of a comprehensive genetic pathway model from a known metabolic pathway database. This model considers the interactions of the by-products, in addition to the main products. Furthermore, we developed a method for the construction of a comprehensive pathway model in a specific organism. In this study, we reconstructed a Saccharomyces cerevisiae model. From this model, the pathways among enzymes that contributed to galactose metabolism were explored. Using S. cerevisiae DNA microarray data, the activated pathways were found among the explored pathways.
Bioinformatics of Profilin in Wheat  [PDF]
Jingming Qu, Xiaohui Zhang, Xingyue Jia, Rong Han
Open Journal of Immunology (OJI) , 2016, DOI: 10.4236/oji.2016.64017
Abstract: Profilin is a small actin-binding protein that is essential in all organisms. While the wheat genome sequence database is not currently available, the exploration of bioinformatics is very important. Therefore, this article predicted the structure and function of profilin in wheat by bioinformatics methods. The amino acid sequence of profilin was searched in GeneBack. While its signal peptides were analyzed through CBS prediction server, the hydrophobicities were analyzed by bioedit software, we used EMBnet server and DNAstar to analyse the transmembrane domains and the B-cell epitopes of the profilin respectively. Finally, the tertiary structure of the protein was predicted through Swiss-Model. This information will help develop rational strategies to improve the component-resolving diagnosis and immunotherapy of profilin allergy.
An Automatic Cross-System File Generation System for Biological Network Visualization Tools  [PDF]
Tianhan Zhang, Xun Lu
Applied Mathematics (AM) , 2014, DOI: 10.4236/am.2014.519296
Abstract: In the field of bioinformatics, the size of a biological network is usually very big. Without any help, it’s extremely hard to analyze the network. If it is shown as a visualized picture, things will be easier. So it’s very important to convert the biological network into a picture. However, there are a lot of software tools to be used to visualize the network. They use different file formats and do not support the transfer from one format to another. Sometimes it’s really hard to deal with it. So I analyzed three text file formats of them (“.dl”, “.net” and “.vna”) and developed a program to do this work automatically. The result of execution is very well and the efficiency is also impressive.
Bioinformatics in Sri Lanka – Still in its infancy
Vajira HW Dissanayake
Sri Lanka Journal of Bio-Medical Informatics , 2013, DOI: http://dx.doi.org/10.4038/sljbmi.v3i1.5072
Abstract: This is the Editorial
Online resources for microRNA analysis
Panagiotis Alexiou,Manolis Maragkakis,Artemis G Hatzigeorgiou
Journal of Nucleic Acids Investigation , 2011, DOI: 10.4081/jnai.2011.e4
Abstract: The use of online tools for bioinformatics analyses is becoming increasingly widespread. Resources specific to the field of microRNAs are available, varying in scope and usability. Online tools are the most useful for casual as well as power users since they need no installation, are hardware independent and are used mostly through graphic user interfaces and links to external sources. Here, we present an overview of useful online resources that have to do with microRNA genomics, gene finding, target prediction and functional analysis.
Ranking small molecules by how much they preferentially inhibit the growth of cancer cell lines with either BRAF or KRAS oncogene mutations
James Langham
PeerJ , 2015, DOI: 10.7287/peerj.preprints.532v1
Abstract: We were interested in the question of whether it might be possible to use knowledge of cancer-related mutations in the cell lines of the NCI60 screening data set to identify small molecules that preferentially inhibit the growth of cell lines containing either BRAF or KRAS oncogene mutations. Our hypothesis was that this cell line mutation knowledge could help to identify small molecules that were more likely to preferentially inhibit growth of cell lines with a particular mutation. It seems that any such molecules might be further investigated to try to better understand the molecular mechanisms of growth inhibition.
Bioinformatics analysis and characteristics of envelop glycoprotein E epitopes of dengue virus  [PDF]
Hua Zhong, Wei Zhao, Liang Peng, Shan-Feng Li, Hong Cao
Journal of Biomedical Science and Engineering (JBiSE) , 2009, DOI: 10.4236/jbise.2009.22022
Abstract: The major envelope glycoprotein E of dengue (DEN) virus plays a central role in the biology of flaviviruses. It is capable of inducing a protective immune response in vivo and responsible for the viral binding to the cellular receptor. The crystal structures of glycoprotein E ectodomains have already been determined. However, it is still un-clear where the well-defined B-cell epitopes for glycoprotein E which induce the neutralizing an-tibodies locates. Thus, in order to characterize the role of glycoprotein E in the pathogenesis of dengue virus infection, we first used network servers (http://bio.dfci. harvard.edu/Tools/ & http://www. imtech. res. in) to predict and analyze the well defined B-cell and T-cell epitopes of the glycoprotein of the DEN-1 HAWAII strain. Then based on the highly conserved envelop glyco-protein amino acids, the hydrophilicity, antigenic-ity, accessibility and flexibility of envelop glyco-protein E were further predicted by using Biotic softwares (DNASTAR) and network servers (http://bio. dfci.harvard.edu/Tools/), the secondary structure was putatively obtained. In our study, the sequence at 281-295 amino acid (aa) for den-gue virus type 1 HAWAII strain and the sequence at 345-359, 383-397 for dengue virus type 2 NGC strain were predicted as the more prevalent epi-topes by using multiple parameters and different analysis softwares, respectively. Two epitopes of DEN-2 and one of DEN-1 locate on the domain Ш and domainⅡ of the protein E, respectively. Sub-sequently, further studies will be carried out to examine the antigenicity and protection of the synthetic peptides with higher scores in the av-erage antigen index (AI) and better hydrophilic properties determined by our data.
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