Hidden stop codons are nucleotide triples TAA, TAG, and TGA that appear in the second and third reading frames of a protein coding gene. Recent studies reported biological evidence suggesting that hidden stop codons a...
详细信息
Hidden stop codons are nucleotide triples TAA, TAG, and TGA that appear in the second and third reading frames of a protein coding gene. Recent studies reported biological evidence suggesting that hidden stop codons are important in preventing misread of mRNA, which is often detrimental to the cell. We study the problem of designing protein-encoding genes with large number of hidden stop codons under biological constraints including GC content and codon usage of individual organism. In simpler models, we obtained provably optimal results. In more complex models, the designed genes have many more hidden stop codons than wild-type genes do, as observed in an experiment with 8 genomes with a wide range of GC content and codon usage.
The rapid growth of the biomedical literature and genomic information presents a major challenge for determining the functional relationships among genes. In this study, we develop a Web-based bioinformatics software ...
详细信息
The rapid growth of the biomedical literature and genomic information presents a major challenge for determining the functional relationships among genes. In this study, we develop a Web-based bioinformatics software environment called FAUN or feature annotation using nonnegative matrix factorization (NMF) to facilitate both the discovery and classification of functional relationships among genes. Both the computational complexity and parameterization of NMF for processing gene sets are discussed. We tested FAUN on three manually constructed gene document collections, and then used it to analyze several microarray-derived gene sets obtained from studies of the developing cerebellum in normal and mutant mice. FAUN provides utilities for collaborative knowledge discovery and identification of new gene relationships from text streams and repositories (e.g., MEDLINE). It is particularly useful for the validation and analysis of gene associations suggested by microarray experimentation.
The breadth of biological data collected in the last decade has far outstripped the methods available to process it. To effectively investigate and explore this abundance of data, novel automated collection and analys...
详细信息
The breadth of biological data collected in the last decade has far outstripped the methods available to process it. To effectively investigate and explore this abundance of data, novel automated collection and analysis approaches must be devised. We have developed a new open software framework, the Open Genomic Analysis Platform (OGAP), to aid in the analysis of genomic data. It is capable of analyzing a variety of data source, and focuses on using information theory to characterize data. The frameworks has is capable of import a variety of genome tied data, and provides custom analysis and visualization of results. We then demonstrate the use of this framework analyzing the Prochlorococcus Marinus organism. We show a strong correlation between the information content of sequence data and up regulation of gene expression during lytic infection.
We discuss how to build systems with sophisticated features based on a core set of bioinformatics tools. Beside from being the front-end server to the core analyses, such a system can manage users, bioinformatics cont...
详细信息
ISBN:
(纸本)9781615677245
We discuss how to build systems with sophisticated features based on a core set of bioinformatics tools. Beside from being the front-end server to the core analyses, such a system can manage users, bioinformatics content and shared data. Using tools available in the open-source community, we show how to build a system with such sophisticated features with a relatively minimal effort, especially in comparison to building such a system from scratch. We discuss the notion of Model-Content Management-View, under whose framework similar applications with such desirable features beyond the field bioinformatics can be built. Our system can be viewed at http://***/rnamotif.
We are given m pursuers and one evader. Each pursuer and the evader has an associated starting point in the plane, a maximum speed, and a start time. We also have a set of line segment obstacles with a total of n endp...
详细信息
Accurate base-assignment in repeat regions of a whole genome shotgun assembly is an unsolved problem. Since reads in repeat regions cannot be easily attributed to a unique location in the genome, current assemblers ma...
详细信息
Current mammographic screeningfor breast cancer is less effective for younger women. To complement mammography for premenopausal women, we investigated the feasibility screening test using 98 blood serum proteins. Bec...
详细信息
In this paper we propose a new method for aligning two RNA secondary structures by taking into account the presence of conserved RNA substructures, or constraints, in the alignment process. Our method allows the incor...
详细信息
We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA...etc), using a...
详细信息
We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA...etc), using a non-redundant dataset of 147 protein chains extracted from protein-RNA complexes in the protein data bank. Our analysis of surface roughness, solid angle and CX value of amino acid residues for each of the protein chains in the dataset shows that: The protein-RNA interface residues tend to be protruding compared to non-interface residues and tend to have higher surface roughness and exhibit moderately convex or concave solid angles. Furthermore, the protein chains in protein-RNA interfaces that contain Viral RNA and rRNA significantly differ from those that contain dsRNA, mRNA siRNA, snRNA, SRP RNA and tRNA with respect to their CX values. The results of this analysis sug gests the possibility of using such structural features to reliably identify protein-RNA interface residues when the structure of the protein is available but the structures of complexes formed by the protein with RNA are not.
暂无评论